Formulation for administration of rna

ABSTRACT

The present invention relates to compositions comprising polyplex formulations for delivery of RNA to a target organ or a target cell after parenteral administration, in particular after intramuscular administration. More precisely, the present invention relates to formulations for administration of RNA such as self-replicating RNA, in particular by intramuscular injection. In more detail, the formulations comprise polyplex particles from single stranded RNA and a polyalkyleneimine. The RNA may encode a protein of interest, such as a pharmaceutically active protein. Furthermore, the present invention relates to pharmaceutical products, comprising said RNA polyplex formulations for parenteral application to humans or to animals. The present invention relates as well to manufacturing of such pharmaceutical products, comprising, optionally, steps of sterile filtration, freezing and dehydration.

TECHNICAL FIELD OF THE INVENTION

The present invention relates to compositions comprising polyplexformulations for delivery of RNA to a target organ or a target cellafter parenteral administration, in particular after intramuscularadministration. More precisely, the present invention relates toformulations for administration of RNA such as self-replicating RNA, inparticular by intramuscular injection. In more detail, the polyplexparticles comprise single stranded RNA, preferably self-replicating orself-amplifying RNA, and a polyalkyleneimine. The RNA may encode aprotein of interest, such as a pharmaceutically active protein. The RNAis taken up by the cell and the RNA is preferably translated into apeptide or protein, which may exhibit its physiological activity. Thecompositions of the invention are applicable for inducing or enhancingan immune response. They are also useful in a prophylactic and/ortherapeutic treatment of a disease involving an antigen such as aprotein. Furthermore, the present invention relates to methods forproducing stable compositions comprising RNA-polyplex formulations, saidRNA-polyplex formulations comprising single stranded RNA and apolyalkyleneimine. RNA-polyplex particle formulations described hereincan be either frozen and thawed, or dehydrated and rehydrated withoutloss of the product quality and, in particular, without substantial lossof RNA activity. In particular, RNA-polyplex particle formulationsdescribed herein can be frozen or dehydrated by freeze drying, spraydrying or related methods, enabling to obtain extended shelf life of theproducts with respect to liquid storage. Furthermore RNA-polyplexparticle formulations described herein may be compliant to therequirements for pharmaceutical products, more specifically referring tothe requirements for GMP manufacturing and the requirements for thequality of pharmaceutical products for parenteral application.RNA-polyplex formulations described herein are in particular useful forvaccination of humans or animals, e.g. against infectious diseases.

BACKGROUND OF THE INVENTION

The introduction of foreign nucleic acids encoding one or morepolypeptides for prophylactic and therapeutic purposes has been a goalof biomedical research for many years. Prior art approaches share thedelivery of a nucleic acid molecule to a target cell or organism, butdiffer in the type of nucleic-acid molecule and/or delivery system:influenced by safety concerns associated with the use ofdeoxyribonucleic acid (DNA) molecules, ribonucleic acid (RNA) moleculeshave received growing attention in the recent years. Various approacheshave been proposed, including administration of single stranded ordouble-stranded RNA, in the form of naked RNA, or in complexed orpackaged form, e.g. in non-viral or viral delivery vehicles. In virusesand in viral delivery vehicles, the nucleic acid is typicallyencapsulated by proteins and/or lipids (virus particle). For example,engineered RNA virus particles derived from RNA viruses have beenproposed as delivery vehicle for treating plants (WO 2000/053780 A2) orfor vaccination of mammals (Tubulekas et al., 1997, Gene, vol. 190, pp.191-195). In view of safety concerns, the medical and veterinarycommunity is reluctant to administer RNA virus particles to humans oranimals. Non-viral delivery vehicles that could be applicable to RNAhave been extensively investigated for development of gene deliverybased therapeutics. However, for various reasons translation ofnon-viral gene delivery approaches into clinical practice has not beenvery successful. Reasons may be associated with unsatisfying levels ofgene expression, technological and regulatory problems related topharmaceutical development of such complex products, and safety reasons.

Thus, there is a need for pharmaceutical products for safe and efficientdelivery of RNA encoding a protein with a therapeutic value, such as avaccine, in patients and animals. As described herein, the aspects andembodiments of the present invention address this need.

SUMMARY OF THE INVENTION

Immunotherapeutic strategies represent promising options for theprevention and therapy of e.g. infectious diseases and cancer diseases.The identification of a growing number of pathogen- and tumor-associatedantigens led to a broad collection of suitable targets forimmunotherapy. The present invention embraces improved agents andmethods suitable for efficient expression of antigens, suitable forimmunotherapeutic treatment for the prevention and therapy of diseases.

In one aspect, the invention relates to a pharmaceutical compositioncomprising:

(a) single stranded RNA; and

(b) polyalkyleneimine.

In a further aspect, the invention relates to a composition comprising:

(a) single stranded RNA; and

(b) polyalkyleneimine

for use as a pharmaceutical.

In one embodiment of all aspects of the invention, the molar ratio ofthe number of nitrogen atoms (N) in the polyalkyleneimine to the numberof phosphor atoms (P) in the single stranded RNA (N:P ratio) is 1.0 to30, preferably 2.0 to 15.0, more preferably 6.0 to 12.0.

In a further aspect, the invention relates to a composition comprising:

(a) single stranded RNA; and

(b) polyalkyleneimine

wherein the molar ratio of the number of nitrogen atoms (N) in thepolyalkyleneimine to the number of phosphor atoms (P) in the singlestranded RNA (N:P ratio) is 1.0 to 30.0, preferably 2.0 to 15.0, morepreferably 6.0 to 12.0.

In one embodiment of all aspects of the invention, the ionic strength ofthe composition is 50 mM or less, preferably wherein the concentrationof positively charged monovalent ions is 25 mM or less and theconcentration of free positively charged divalent cationic ions is 20 μMor less.

In a further aspect, the invention relates to a composition comprising:

(a) single stranded RNA; and

(b) polyalkyleneimine

wherein the ionic strength is 50 mM or less.

In one embodiment, the concentration of positively charged monovalentions is 25 mM or less and the concentration of positively chargeddivalent cationic ions is 20 μM or less.

In one embodiment of all aspects of the invention, the composition isfor intramuscular administration such as by intramuscular injection.

In one embodiment of all aspects of the invention, the single strandedRNA and the polyalkyleneimine are present in polyplex particles.

In one embodiment of all aspects of the invention, the polyalkyleneiminecomprises the following general formula (I):

wherein

R is H, an acyl group or a group comprising the following generalformula (II):

wherein R₁ is H or a group comprising the following general formula(III):

n, m, and l are independently selected from integers from 2 to 10; and

p, q, and r are integers, wherein the sum of p, q, and r is such thatthe average molecular weight of the polymer is 1.5-10² to 10⁷ Da,preferably 5000 to 105 Da, more preferably 10000 to 40000 Da, morepreferably 15000 to 30000 Da, even more preferably 20000 to 25000 Da.

In one embodiment, n, m, and l are independently selected from 2, 3, 4,and 5, preferably from 2 and 3. In one embodiment, R₁ is H. In oneembodiment, R is H or an acyl group.

In one embodiment of all aspects of the invention, the polyalkyleneiminecomprises polyethylenimine and/or polypropyleneimine, preferablypolyethyleneimine.

In one embodiment of all aspects of the invention, at least 92% of the Natoms in the polyalkyleneimine are protonatable.

In one embodiment of all aspects of the invention, the composition ofthe invention comprises one or more additives. In one embodiment, theone or more additives are selected from the group consisting ofbuffering substances, saccharides, stabilizers, cryoprotectants,lyoprotectants, and chelating agents. In one embodiment of all aspectsof the invention, the composition of the invention comprises one or morepolymers. In one embodiment, the buffering substances comprise at leastone selected from the group consisting of4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES),2-(N-morpholino)ethanesulfonic acid (MES),3-morpholino-2-hydroxypropanesulfonic acid (MOPSO), acetic acidbuffering systems and analogues, phosphatic acid buffering systems, orcitric acid buffering systems. In one embodiment of all aspects of theinvention, the composition of the invention comprises buffers forbuffering in the pH range between 4 and 8, preferably between 5 and 7.5.Examples for such buffer systems are acetate buffers or HEPES buffers orphosphate buffers or acetic acid buffers. In one embodiment, thesaccharides comprise at least one selected from the group consisting ofmonosaccharides, disaccharides, trisaccharides, oligosaccharides, andpolysachharides, preferably from glucose, trehalose, saccharose anddextran. In one embodiment, the additive is a dextran with a mean molarmass between 1 kDa and 100 kDa. In one embodiment, the cryoprotectantscomprise at least one selected from the group consisting of glycols,such as ethylene glycol, propylene glycol, and glycerol. In oneembodiment, the chelating agent comprises EDTA. In one embodiment, thelipids comprise at least one selected from the group consisting ofcationic lipids, neutral lipids, and anionic lipids. In one embodiment,the composition of the invention comprises one or more block copolymerscomprising ethylene oxide and propylene oxide building blocks. In oneembodiment, the composition of the invention comprises copolymerscomprising ethylene diamine groups. In one embodiment, the compositionof the invention comprises an amphiphilic block copolymer, preferablycomprising ethylene oxide and propylene oxide building blocks,optionally comprising also ethylene diamine groups.

In one embodiment of all aspects of the invention, the compositioncomprises HEPES buffered glucose (HBG or HBGx1), MES-buffered glucose(MBG or MBGx1) or HEPES buffered trehalose (HBT or HBTx1). In oneembodiment of all aspects of the invention, the composition comprisesglucose or trehalose or saccharose in an acetic acid buffer with aconcentration in the range from 0.1 mM to 10 mM. In one embodiment ofall aspects of the invention, the composition comprises glucose ortrehalose or saccharose in a phosphate buffer with a concentration inthe range from 0.1 mM to 10 mM.

In one embodiment of all aspects of the invention, the z-average size ofthe particles is less than 200 nm, preferably less than 150 nm and morepreferably less than 100 nm. In one embodiment, the z-average size ofthe particles is between 50 nm and 200 nm. In one embodiment of allaspects of the invention, the Zeta-potential of the particles is 20 mVor more, preferably 25 to 40 mV. In one embodiment of all aspects of theinvention, the electrophoretic mobility (p) of the particles is between1 to 1.6 μm*cm/V*S. In one embodiment of all aspects of the invention,the z-average size of the particles and/or the Zeta-potential and/or theelectrophoretic mobility are determined in a suspension comprising thepolyplex particles and HEPES buffered glucose (HBG) or HEPES bufferedtrehalose (HBT). In one embodiment, the HBG comprises 5% glucose (w/v)and 10 mM HEPES, pH 7.1 or the HBT comprises 10% trehalose (w/v) and 10mM HEPES, pH 7.1. In one embodiment, the z-average size of the particlesis determined by dynamic light scattering and data analysis by cumulantalgorithm. In one embodiment, the translation diffusion coefficient ismeasured by dynamic light scattering. Then, Stock-Einstein equation isused in order to calculate the Z-average. In one embodiment, theelectrophoretic mobility is measured by laser-Doppler electrophoresis.Then, Henry equation or Smoluchowski equation is used in order tocalculate the Zeta-potential.

In one embodiment of all aspects of the invention, the particles areneutral or positively charged, preferably at physiological pH or at a pHbetween 4.5 and 7.5.

In one embodiment of all aspects of the invention, the single strandedRNA is a molecule of 6000 to 15000 bases, preferably 9000 to 12000bases. In one embodiment of all aspects of the invention, the singlestranded RNA encodes at least one protein of interest. In one embodimentof all aspects of the invention, the single stranded RNA is a replicon,preferably self-replicating or self-amplifying RNA. In one embodiment,the replicon can be replicated by a replicase from an alphavirus, andwherein the replicon preferably comprises a 5′ replication recognitionsequence from an alphavirus, or a variant thereof, and a 3′ replicationrecognition sequence from an alphavirus, or a variant thereof. In oneembodiment of all aspects of the invention, the single stranded RNAcomprises an open reading frame encoding a peptide or protein ofinterest such as a pharmaceutically active peptide or protein.

In one embodiment of all aspects of the invention, the compositiondescribed herein is for use in therapy. In one embodiment of all aspectsof the invention, the composition described herein is a vaccinecomposition.

In a further aspect, the invention relates to a use of a compositiondescribed herein for introducing RNA into a cell, in particular forexpressing RNA in a cell. In one embodiment, the cell is a muscle cell.

In a further aspect, the invention relates to a use of a compositiondescribed herein for intramuscular administration of RNA.

In a further aspect, the invention relates to a method of intramuscularadministration of RNA comprising the step of intramuscularlyadministering the composition described herein.

In a further aspect, the invention relates to a frozen, lyophilized orspray dried composition comprising:

(a) single stranded RNA; and

(b) polyalkyleneimine

wherein the composition comprises a cryoprotectant and/or lyoprotectant,preferably a disaccharide such as trehalose, or a polysaccharide such asdextran.

In one embodiment, the composition further comprises a chelating agentsuch as EDTA.

In one embodiment, the composition is prepared from an aqueouscomposition comprising a disaccharide at 5-20% (w/v) and optionally thechelating agent at 20 μM to 10 mM such as 80 μM to 5 mM. In oneembodiment, the aqueous composition comprises trehalose, HEPES, and EDTAsuch as 10% trehalose (w/v), 2.8 mM HEPES, 80 μM EDTA, pH 7.1.

In a further aspect, the invention relates to an aqueous compositionobtainable by thawing the frozen composition described herein orreconstituting the lyophilized or spray dried composition describedherein.

In a further aspect, the invention relates to a method of preparing afrozen, lyophilized or spray dried composition comprising:

(i) preparing an aqueous composition comprising single stranded RNA,polyalkyleneimine and a cryoprotectant and/or lyoprotectant, preferablya disaccharide such as trehalose, or a polysaccharide such as dextranand

(ii) freezing, lyophilizing or spray drying the composition.

In one embodiment, the aqueous composition further comprises a chelatingagent such as EDTA. In one embodiment, the aqueous composition comprisesthe disaccharide at 5-20% (w/v) and optionally the chelating agent at 20μM to 10 mM such as 80 μM to 5 mM. In one embodiment, the aqueouscomposition comprises trehalose, HEPES, and EDTA such as 10% trehalose(w/v), 2.8 mM HEPES, 80 μM EDTA, pH 7.1.

In a further aspect, the invention relates to a use of a cryoprotectantand/or lyoprotectant, preferably a disaccharide such as trehalose, or apolysaccharide such as dextran for preparing a frozen, lyophilized orspray dried composition comprising:

(a) single stranded RNA; and

(b) polyalkyleneimine.

In one embodiment, the disaccharide is used in combination with achelating agent such as EDTA.

The frozen or lyophilized or spray dried composition or the aqueouscomposition for preparing the frozen or lyophilized or spray driedcomposition may comprise one or more of the following:

(i) Non-aqueous solvents such as ethylene glycol, glycerol,dimethylsulphoxide, and dimethylformamide.

(ii) Surfactants such as Tween 80, Brij 35, Brij 30, Lubrol-px, TritonX-10; Pluronic F127 (polyoxyethylene-polyoxypropylene copolymer) alsoknown as poloxamer, poloxamine, and sodium dodecyl sulfate.

(iii) Disaccharides such as trehalose, sucrose, lactose, and maltose.

(iv) Polymers (which may have different MWs) such as polyethyleneglycol, dextran, poly(vinyl alcohol), hydroxypropyl methylcellulose,gelatin, polyvinylpyrrolidone, hydroxyethyl cellulose, Ficoll, andalbumin.

(v) Amino acids such as glycine, proline, 4-hydroxyproline, L-serine,glutamate, alanine, lysine, sarcosine, and gamma-aminobutyric acid.

In a further aspect, the invention relates to a method for continuousflow manufacturing of RNA polyplex formulations by using continuous flowpumps and a mixing device, where two aqueous fluids are mixed by mm orμm sized channels.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1. A. Toxicity of free pure PEI on HEK-293 cells in-vitro. IC₅₀=77μM of nitrogens (free). B. Toxicity of PEI/Replicon-RNA polyplexes onHEK-293 cells in-vitro. IC₅₀=542 μM of nitrogens (polyplex formulation).

FIG. 2. Relative luminescence from C2C12 muscle cells after incubationwith PEI/Replicon-RNA polyplexes at N/P 11.6 from different storageconditions after 1 week storage.

FIG. 3. Relative RNA integrity of PEI/Replicon-RNA polyplexes at N/P11.6 at different storage conditions after 2 weeks storage.

FIG. 4. poly(2-ethyl-2-oxazoline) is obtained by a ring-openingisomerization polymerization of 2-ethyl-2-oxazoline in the presence ofinitiators.

FIG. 5. Synthesis of fully deacylated linear PE122, PE187, and PE1217 bythe acid hydrolysis of PEOZs. Conditions: (i) 24% (wt/vol) HCl, 110° C.,96 h; n=504 for 50-kDa PEOZ, 2,018 for 200-kDa PEOZ, and 5,044 for500-kDa PEOZ.

FIG. 6. Aggregation kinetics of IVT (A) and Replicon (B) polyplexes atincreasing salt concentrations.

FIG. 7. Physicochemical parameters of polyplexes before (initial) andafter (final) the filtration. A and B. The diameter and thepolydispersity of the polyplexes were measured by DLS. C. RNA wasreleased from the polyplexes by Heparin, and measured by UV absorptionat 260 nm. D. PEI concentration was measured by CuSO₄ assay.

FIG. 8. Comparison of the chemical structures of highly pure PEI andregular purity PEI. n=58 for PEI of 25 kDa. The average number of the—CH2CH2NH— monomers in PEI 25 kD is 581, which is also the length of thecontiguous stretch of potentially protonatable nitrogens. Assuming auniform distribution of the N-propionyl moieties in the regular PE125,its contiguous stretch of protonatable nitrogens is only 64.

FIG. 9. Transfection of C2C12 muscle cells in-vitro by Replicon-RNApolyplexes that were prepared using PEIs of different purity level atdifferent N/P ratios.

FIG. 10. Replicon-RNA Polyplexes at N/P ratios of 1 (−) and 11.6 (+)were prepared with highly pure PEI (jetPEI) and regular purity PEI (25kDa). Free RNA was used as a control. The formulations were injectedi.m. to the posterior limbs of the mice (n=3). Luminescence signals wererecorded from the muscles of the mice.

FIG. 11. Replicon-RNA Polyplexes at N/P ratios of 7.7 and 11.6 wereprepared with highly pure PEIs: jetPEI (from Polyplus), PEI-Max 40000(from Polyscience), and Exgen 500 (from Eurodamex). All formulationswere prepared in HBGx1 buffer except of the lyophilized formulation,which was prepared in HBTx1 buffer. The formulations were injected i.m.to the posterior limbs of the mice (n=3). Luminesence signals wererecorded from the muscles of the mice.

FIG. 12. Lyophilized cakes of JetPEI/Replicon-RNA polyplexes at N/P 11.6prepared with different buffers.

FIG. 13. C2C12 muscle cells were transfected in-vitro by IVT-RNA thatencodes for luciferase. The RNA was complexes with JetPEI at differentN/P ratios in HBGx1 buffer. Luminescence signal was measured 24 h afterthe transfection.

FIG. 14. IVT-RNA Polyplexes at N/P ratios of 5.8 and 11.6 were preparedwith pure PEI in HBGx1 buffer. Free IVT-RNA in HBGx1 buffer was used asa control. The formulations were injected i.m. to the posterior limbs ofthe mice (n=3) at RNA doses of 2-8 μg per injection. Luminesence signalswere recorded from the muscles of the mice 6 h after the injection.

FIG. 15. Polyplexes of Replicon-RNA and jetPEI were prepared atdifferent RNA concentration at N/P ratio 11.6 in HBGx1 buffer. For sizemeasurements by DLS the polyplexes were diluted to RNA concentration of10 mg/l.

FIG. 16. C2C12 muscle cells were transfected in-vitro by the polyplexesfrom FIG. 16. The luminescence signal was measured 24 h after thetransfection.

FIG. 17. Rep-RNA Polyplexes at N/P ratio 11.6 were prepared with purePEI in HBGx1 buffer at different RNA concentration as in FIG. 16. Theformulations were injected i.m. to the posterior limbs of the mice (n=3)at RNA doses of 2-8 μg per injection. Luminesence signals were recordedfrom the muscles of the mice.

FIG. 18. In-vitro studies with PEI/Replicon-RNA polyplexes on humanDendritic cells (DCs) and mouse muscle cells (C2C12) A. Toxicity(expressed as % of viable cells after treatment with polyplexes) B.Transfection (expressed as luminescence emission after treatment withpolyplexes). The transfection results are shown only for C2C12 cells.

FIG. 19. Rep-RNA Polyplexes at N/P ratios 11.6 or 15.8 were preparedwith PEI from Polyplus or Polytheragene in HBGx1 or Hepes 10 mM buffers.Before injection to mice the polyplexes were diluted in HBGx1 orOpti-MEM buffers. The formulations were injected i.m. to the posteriorlimbs of the mice (n=3) at RNA doses of 2 μg per injection. Luminesencesignals were recorded from the muscles of the mice.

FIG. 20. A) Four, seven and eleven days after intramuscular (i.m.)application of 2 μg non-formulated (buffer solution) or formulatedReplicon-RNA encoding Luciferase to both musculus tibialis posterior ofBalb/c mice, the animals were subjected to non-invasive in vivobioluminescence imaging. Photons deriving from Luciferase protein werecollected over one minute and are shown as an overlay with thephotograph of the imaged mice. B) Graphical display of measuredphotons/second (p/s) at injection site.

FIG. 21. A) Seven days after intradermal (i.d.) application of 2 μgnon-formulated (buffer solution) or formulated Replicon-RNA encodingLuciferase to two injection sites at the dorsal skin of Balb/c mice, theanimals were subjected to non-invasive in vivo bioluminescence imaging.Photons deriving from Luciferase protein were collected over one minuteand are shown as an overlay with the photograph of the imaged mice.Black arrows indicate the site of injection. B) Graphical display ofmeasured photons/second (p/s) at injection site.

FIG. 22. Beneficial effect of Replicon-RNA formulation as a vaccine

FIG. 23. Beneficial effect of Replicon-RNA formulation as a vaccine

FIG. 24. Results from Spray drying of Replicon-RNA formulated with PEIin 10% (w:v) Trehalose

FIG. 25. Normalized luminescence from C2C12 muscle cells afterincubation with PEI/Replicon-RNA polyplexes at different N/P ratio,before (Prepared) and after (Sterilized) sterile filtration.

FIG. 26: Effect of combination of Short and Long PEI on transfectionefficiency in vitro according to example 16. FIG. 26 A): transfectionefficacy of Short linear PEI and Long PEI polyplexes at 250 ng ofRNA/well. FIG. 26 B): transfection efficacy of short branched PEI andlong PEI polyplexes at 250 ng of RNA/well. Compared to the benchmark invivo Jet PEI and for the same total NP ratio, higher expression levelsin different time frames were achieved with combinations of Short PEI(FIG. 26 A: linear; FIG. 26 B: branched) and Long PEI (e.g. in vivojetPEI).

FIG. 27: Replicon-RNA Transfection efficacy of Long Jet PEI+Short PEIPolyplexes versus Benchmark (i.e. in vivo JetPEI NP12) according toexample 17: Short PEI (branched 1.8 kDA) and Long PEI at differentcombinations (NP4+NP8 or NP1,15+NP11) for a total NP of 12.

FIG. 28: Effect of salt variations (e.g. NaCl) on Replicon (saRNA)-RNAtransfection efficiency in vivo according to example 18. Bioluminescencesignals were detected at day 3 (FIG. 28A), 6 (FIG. 28B), 9 (FIG. 28C)and 13 (FIG. 28D). Signal strength was compared in FIG. 28E. The mostintense signal in muscle region of mice could be detected at day 6 afteri.m. injection in mice receiving PEI-Replicon-RNA polyplexes (e.g. LongPEI N/P 12) and addition of low concentrations (5 to 10 mM) salt.

FIG. 29: Effect of pH adjustments on transfection efficiency of Replicon(saRNA)-PEI formulations according to example 18. Good results wereobtained with saRNA-PEI polyplex formulations having pH values between6.5 and 7.1. The most intense signal could be detected with a saRNA-longPEI NP12 formulation adjusted to pH 6.5. As benchmarks, saRNA-Jet PEIPolyplexes NP12 with unadjusted pH (BM) or HBG (20 mM Hepes, pH 7.4, 5wt. % glucose) were used.

FIG. 30: Electrophoretic mobility of in vivo jetPEI/Replicon-RNApolyplexes (N/P 4) adjusted to different pH values according to example19.

FIG. 31: Normalized luminescence from C2C12 muscle cells afterincubation with different dosages of in vivo jetPEI/Replicon-RNApolyplexes at a N/P ratio of 4 and different pH values (pH 6.5-pH 8.5)according to example 19.

FIG. 32: Luciferase expression after transfection with different amountsof PEI/excess of positive charges in PEI formulations according toexample 20.

FIG. 33: Optimizing the polyplex transfection by using 2-Stepcomplexation according to example 21.

FIG. 34: Immunization experiment according to example 22 showing thesuperior effect of saRNA-polyplexes formulated with MES-buffered glucose(MBG) in comparison to HEPES-buffered glucose (HBG).

DETAILED DESCRIPTION OF THE INVENTION

Although the present invention is described in detail below, it is to beunderstood that this invention is not limited to the particularmethodologies, protocols and reagents described herein as these mayvary. It is also to be understood that the terminology used herein isfor the purpose of describing particular embodiments only, and is notintended to limit the scope of the present invention which will belimited only by the appended claims. Unless defined otherwise, alltechnical and scientific terms used herein have the same meanings ascommonly understood by one of ordinary skill in the art.

Preferably, the terms used herein are defined as described in “Amultilingual glossary of biotechnological terms: (IUPACRecommendations)”, H. G. W. Leuenberger, B. Nagel, and H. Kölbl, Eds.,Helvetica Chimica Acta, CH-4010 Basel, Switzerland, (1995).

The practice of the present invention will employ, unless otherwiseindicated, conventional methods of chemistry, biochemistry, cellbiology, immunology, and recombinant DNA techniques which are explainedin the literature in the field (cf., e.g., Molecular Cloning: ALaboratory Manual, 2nd Edition, J. Sambrook et al. eds., Cold SpringHarbor Laboratory Press, Cold Spring Harbor 1989).

In the following, the elements of the present invention will bedescribed. These elements are listed with specific embodiments, however,it should be understood that they may be combined in any manner and inany number to create additional embodiments. The variously describedexamples and preferred embodiments should not be construed to limit thepresent invention to only the explicitly described embodiments. Thisdescription should be understood to disclose and encompass embodimentswhich combine the explicitly described embodiments with any number ofthe disclosed and/or preferred elements. Furthermore, any permutationsand combinations of all described elements in this application should beconsidered disclosed by this description unless the context indicatesotherwise.

The term “about” means approximately or nearly, and in the context of anumerical value or range set forth herein preferably means+/−10% of thenumerical value or range recited or claimed.

The terms “a” and “an” and “the” and similar reference used in thecontext of describing the invention (especially in the context of theclaims) are to be construed to cover both the singular and the plural,unless otherwise indicated herein or clearly contradicted by context.Recitation of ranges of values herein is merely intended to serve as ashorthand method of referring individually to each separate valuefalling within the range. Unless otherwise indicated herein, eachindividual value is incorporated into the specification as if it wasindividually recited herein. All methods described herein can beperformed in any suitable order unless otherwise indicated herein orotherwise clearly contradicted by context. The use of any and allexamples, or exemplary language (e.g., “such as”), provided herein isintended merely to better illustrate the invention and does not pose alimitation on the scope of the invention otherwise claimed. No languagein the specification should be construed as indicating any non-claimedelement essential to the practice of the invention.

Unless expressly specified otherwise, the term “comprising” is used inthe context of the present document to indicate that further members mayoptionally be present in addition to the members of the list introducedby “comprising”. It is, however, contemplated as a specific embodimentof the present invention that the term “comprising” encompasses thepossibility of no further members being present, i.e. for the purpose ofthis embodiment “comprising” is to be understood as having the meaningof “consisting of”.

Several documents are cited throughout the text of this specification.Each of the documents cited herein (including all patents, patentapplications, scientific publications, manufacturer's specifications,instructions, etc.), whether supra or infra, are hereby incorporated byreference in their entirety. Nothing herein is to be construed as anadmission that the present invention was not entitled to antedate suchdisclosure.

In the following, definitions will be provided which apply to allaspects of the present invention.

Terms such as “reduce” or “inhibit” as used herein means the ability tocause an overall decrease, preferably of 5% or greater, 10% or greater,20% or greater, more preferably of 50% or greater, and most preferably75% or greater, in the level. The term “inhibit” or similar phrasesincludes a complete or essentially complete inhibition, i.e. a reductionto zero or essentially to zero.

Terms such as “increase” or “enhance” preferably relate to an increaseor enhancement by about at least 10%, preferably at least 20%,preferably at least 30%, more preferably at least 40%, more preferablyat least 50%, even more preferably at least 80%, and most preferably atleast 100%.

“Fragment”, with reference to a nucleic acid sequence, relates to a partof a nucleic acid sequence, i.e. a sequence which represents the nucleicacid sequence shortened at the 5′- and/or 3′-end(s). Preferably, afragment of a nucleic acid sequence comprises at least 80%, preferablyat least 90%, 95%, 96%, 97%, 98%, or 99% of the nucleotide residues fromsaid nucleic acid sequence. In the present invention those fragments ofRNA molecules are preferred which retain RNA stability and/ortranslational efficiency.

“Fragment”, with reference to an amino acid sequence (peptide orprotein), relates to a part of an amino acid sequence, i.e. a sequencewhich represents the amino acid sequence shortened at the N-terminusand/or C-terminus. A fragment shortened at the C-terminus (N-terminalfragment) is obtainable e.g. by translation of a truncated open readingframe that lacks the 3′-end of the open reading frame. A fragmentshortened at the N-terminus (C-terminal fragment) is obtainable e.g. bytranslation of a truncated open reading frame that lacks the 5′-end ofthe open reading frame, as long as the truncated open reading framecomprises a start codon that serves to initiate translation. A fragmentof an amino acid sequence comprises e.g. at least 1%, at least 2%, atleast 3%, at least 4%, at least 5%, at least 10%, at least 20%, at least30%, at least 40%, at least 50%, at least 60%, at least 70%, at least80%, at least 90% of the amino acid residues from an amino acidsequence.

The term “ionic strength” refers to the mathematical relationshipbetween the number of different kinds of ionic species in a particularsolution and their respective charges. Thus, ionic strength I isrepresented mathematically by the formula

$I = {\frac{1}{2}\underset{i}{\cdot \sum}{z_{i}^{2} \cdot c_{i}}}$

in which c is the molar concentration of a particular ionic species andz the absolute value of its charge. The sum Σ is taken over all thedifferent kinds of ions (i) in solution.

It is preferred that the ionic strength of the compositions describedherein is 50 mM or less, preferably 25 mM or less, preferably 20 mM orless, 19 mM or less, 18 mM or less, 17 mM or less, 16 mM or less, 15 mMor less, 10 mM or less, or 5 mM or less. Preferably, the ionic strengthof the compositions described herein is low enough so as to preventaggregation of polyplex particles.

According to the invention, the term “ionic strength” preferably relatesto the presence of monovalent ions. Regarding the presence of divalentions, in particular divalent cations, their concentration or effectiveconcentration (presence of free ions) due to the presence of chelatingagents is preferably sufficiently low so as to prevent degradation ofthe RNA. In one particularly preferred embodiment, the concentration oreffective concentration of divalent ions is below the catalytic levelfor hydrolysis of the phosphodiester bonds between RNA nucleotides. Inone particularly preferred embodiment, the concentration of freedivalent ions is 20 μM or less, preferably there are no or essentiallyno free divalent ions.

It is preferred that the pH of the compositions described herein isbetween 4 and 8; more preferably between 5.5 and 8 such as between 6 and7.5, e.g. between 6.5 and 7.1, between 6.5 and 7, or between 6.5 and6.9.

The term “disaccharide” refers to carbohydrates composed of twomonosaccharide residues linked by glycosidic bonds. Representativeexamples of disaccharides include trehalose, maltose, sucrose, lactose,lactulose, cellobiose, isomaltose, gentibiose, laminarin disaccharide(laminarabiose), chitobiose, xylobiose (xylobiose), inulin disaccharideand mannobiose sugar. A preferred content of the disaccharide in thecompositions described herein is 5-20% (w/v) such as 5-15% (w/v), 7-15%(w/v) or 8-12% (w/v). Preferred according to the invention aredisaccharides having high glass transition temperatures.

The term “chelating agent” means a compound which forms a chelate withmetal ions, preferably divalent or multivalent metal ions. A chelatingagent has a plurality of groups, e.g., OH, —COOH, capable of forming aring structure with metal ions. Examples of chelating agents are:ethylene diamine tetraacetic acid (EDTA), diethylene triaminepentaacetic acid (DTPA), trans-1,2-diamino-cyelohexane tetraacetic acidmonohydrate, N-hydroxyethylethylene diamine triacetic acid (HEDTA)citric acid, and phosphoric acid chelating agents (e.g., Dequest 2000).Ethylene diamine tetraacetic acid (EDTA) is preferred according to theinvention. It is preferred that the chelating agent is present in thecompositions described herein in a concentration of at least 20 μM, atleast 40 μM, at least 60 μM, or at least 80 μM. It is preferred that thechelating agent is present in the compositions described herein in aconcentration of up to 10 mM, up to 5 mM, up to 2 mM, up to 1 mM, up to0.5 mM, up to 0.2 mM, or up to 0.1 mM.

The term “freezing” relates to the solidification of a liquid, usuallywith the removal of heat.

The term “lyophilizing” or “lyophilization” refers to the freeze-dryingof a substance by freezing it and then reducing the surrounding pressureto allow the frozen medium in the substance to sublimate directly fromthe solid phase to the gas phase.

The term “spray drying” refers to spray drying a substance by mixing(heated) gas with a fluid that is atomized (sprayed) within a vessel(spray dryer), where the solvent from the formed droplets evaporates,leading to a dry powder.

The term “cryoprotectant” relates to a substance that is added to aformulation in order to protect the active ingredients during thefreezing stages.

The term “lyoprotectant” relates to a substance that is added to aformulation in order to protect the active ingredients during the dryingstages.

The term “reconstitute” relates to adding a solvent such as water to adried product to return it to a liquid state such as its original liquidstate.

The term “autologous” is used to describe anything that is derived fromthe same subject. For example, “autologous cell” refers to a cellderived from the same subject. Introduction of autologous cells into asubject is advantageous because these cells overcome the immunologicalbarrier which otherwise results in rejection.

The term “allogeneic” is used to describe anything that is derived fromdifferent individuals of the same species. Two or more individuals aresaid to be allogeneic to one another when the genes at one or more lociare not identical.

The term “syngeneic” is used to describe anything that is derived fromindividuals or tissues having identical genotypes, i.e., identical twinsor animals of the same inbred strain, or their tissues or cells.

The term “heterologous” is used to describe something consisting ofmultiple different elements. As an example, the introduction of oneindividual's cell into a different individual constitutes a heterologoustransplant. A heterologous gene is a gene derived from a source otherthan the subject.

According to the invention, owing to the instability of non-protectedRNA, it is advantageous to provide the RNA molecules in complexed form.In particular, in some embodiments, the compositions of the presentinvention comprise particles comprising RNA and polyalkyleneimine.

When the system according to the present invention is formulated as aparticulate formulation, it is possible that each RNA species (e.g.replicon, replicase construct, and optional additional RNA species suchas an RNA encoding a protein suitable for inhibiting IFN) is separatelyformulated as an individual particulate formulation. In that case, eachindividual particulate formulation will comprise one RNA species. Theindividual particulate formulations may be present as separate entities,e.g. in separate containers. Such formulations are obtainable byproviding each RNA species separately (typically each in the form of anRNA-containing solution) together with a particle-forming agent, therebyallowing the formation of particles. Respective particles will containexclusively the specific RNA species that is being provided when theparticles are formed (individual particulate formulations).

In one embodiment, a composition according to the invention comprisesmore than one individual particle formulation. Respective compositionsare referred to as mixed particulate formulations. Mixed particulateformulations according to the invention are obtainable by forming,separately, individual particulate formulations, as described above,followed by a step of mixing of the individual particulate formulations.By the step of mixing, a formulation comprising a mixed population ofRNA-containing particles is obtained (for illustration: e.g. a firstpopulation of particles may contain replicon, and a second formulationof particles may contain replicase construct). Individual particulatepopulations may be together in one container, comprising a mixedpopulation of individual particulate formulations.

Alternatively, it is possible that all RNA species of the composition(e.g. replicon, replicase construct, and optional additional speciessuch as RNA encoding a protein suitable for inhibiting IFN) areformulated together as a combined particulate formulation. Suchformulations are obtainable by providing a combined formulation(typically combined solution) of all RNA species together with aparticle-forming agent, thereby allowing the formation of particles. Asopposed to a mixed particulate formulation, a combined particulateformulation will typically comprise particles which comprise more thanone RNA species. In a combined particulate composition different RNAspecies are typically present together in a single particle.

In one embodiment, the particulate formulation of the present inventionis a nanoparticulate formulation. In that embodiment, the compositionaccording to the present invention comprises RNA in the form ofnanoparticles.

In a general definition, the term “nanoparticle” refers to any particlehaving a diameter of between 1 nm and 1000 nanometers (nm).

In the context of the present invention, the term “particle” relates toa structured entity formed by molecules or molecule complexes. In oneembodiment, the term “particle” relates to a micro- or nano-sizedstructure, such as a micro- or nano-sized compact structure.

The terms “In vivo-jetPEI™”, “in vivo jetPEI™”, “in vivo jetPEI”,“jetPEI”, “jet PEI”, and “JetPEI” all refer to commercially available Invivo-jetPEI™ Reagent, Cat. #201-50G from Polyplus-Transfection SA(Illkirch, France).

The term “polyplex” as used herein refers to a complex of a polymer anda nucleic acid such as RNA formed via electrostatic interactions. Incases where the polyplex comprises RNA, it may be also referred to as“RNA complex” or “RNA polyplex”.

The present invention relates to polyplex particles formed from at leastone single stranded RNA and at least one polyalkyleneimine.

In one embodiment, the particles described herein have an averagediameter less than about 200 nm, preferably less than about 150 nm, andmore preferably less than about 100 nm. In one embodiment, the particlesdescribed herein have an average diameter of at least about 30 nm, atleast about 40 nm, at least about 50 nm, at least about 60 nm, at leastabout 70 nm, at least about 80 nm, at least about 90 nm, or at leastabout 100 nm.

The term “average diameter” refers to the mean hydrodynamic diameter ofthe particles as measured by dynamic light scattering with data analysisusing the so-called cumulant algorithm, which provides as results theso-called Z_(average) with the dimension of a length, and thepolydispersity index (PI), which is dimensionless (Koppel, D., J. Chem.Phys. 57, 1972, pp 4814-4820, ISO 13321). Here “average diameter”,“diameter” or “size” for particles is used synonymously with this valueof the Z_(average).

The term “net charge” relates to the total sum of charges, such aspositive and negative charges. For example, if a particle comprises ahigher number of negative charges than positive charges, the net chargeof the particle is negative. If the particle comprises a higher numberof positive charges than negative charges, the net charge of theparticle is positive. If the particle comprises an equal number ofpositive charges and negative charges, the net charge of the particle isneutral, particularly electroneutral. Thus, the net charge of theparticle according to the present invention can be negative, positive orneutral. In one embodiment, the net charge of the particle is positive.In one embodiment, the net charge of the particle is negative.

Terms as “charged”, “net charge”, “negatively charged” or “positivelycharged” refer to the electric net charge of the given compound orparticle when dissolved or suspended in aqueous buffer at the relevantpH (e.g., 7.1).

According to the present invention, the terms “N/P ratio”, “NP ratio”,“N:P ratio”, “N/P” and “NP” refer to the molar ratio of nitrogen atoms(N) in the polyethyleneimine to phosphor atoms (P) in the RNA.

According to the invention, the molar ratio of the number of nitrogenatoms (N) in the polyalkyleneimine to the number of phosphor atoms (P)in the RNA (N/P ratio) is preferably 2.0 to 15.0, preferably 8.0 to12.0, 6.0 to 14.0 or 6.0 to 12.0.

According to the invention, it is preferred to adjust the compositionsdescribed herein to the final N/P ratio in more than 1 step, such as in2, 3, 4, or more steps. For example, the composition may be adjusted toa first N/P ratio which is lower than the final N/P ratio in a firststep, for example, using a long polyalkyleneimine. By adding furtherpolyalkyleneimine, for example, short polyalkyleneimine or longpolyalkyleneimine such as the long polyalkyleneimine used in the firststep, the N/P ratio may be adjusted to the final N/P ratio. In oneembodiment, the final N/P ratio is between 8 and 16, such as between 9and 14, e.g., between 10 and 12. In one embodiment, the N/P ratioresulting in the first step is between 1 and 6 such as between 2 and 5such as 3 or 4.

Polyalkyleneimines

The polyalkyleneimine as used herein preferably comprises the followinggeneral formula (I):

wherein

R is H, an acyl group or a group comprising the following generalformula (II):

wherein R₁ is H or a group comprising the following general formula(III):

n, m, and l are independently selected from integers from 2 to 10; and

p, q, and r are integers, wherein the sum of p, q, and r is such thatthe average molecular weight of the polymer is 1.5-10² to 10⁷ Da,preferably 5000 to 105 Da, more preferably 10000 to 40000 Da, morepreferably 15000 to 30000 Da, even more preferably 20000 to 25000 Da.

In one embodiment, n, m, and l are independently selected from 2, 3, 4,and 5, preferably from 2 and 3, and more preferably are 2. In oneembodiment, R₁ is H. In one embodiment, R is H or an acyl group.

In one embodiment, the polyalkyleneimine comprises polyethylenimineand/or polypropyleneimine, preferably polyethyleneimine. A preferredpolyalkyleneimine is polyethyleneimine (PEI). The average molecularweight of PEI is preferably 1.5·10² to 10⁷ Da, preferably 5000 to 105Da, more preferably 10000 to 40000 Da, more preferably 15000 to 30000Da, even more preferably 20000 to 25000 Da.

Preferred according to the invention is linear polyalkyleneimine such aslinear polyethyleneimine (PEI). In one embodiment, linear PEI isobtained by a ring-opening isomerization polymerization of2-ethyl-2-oxazoline to obtain poly(2-ethyl-2-oxazoline) (PEOX;N-propionyl-PEI), which is then acid-hydrolyzed to cleave off theN-propionyl groups to yield PEI.

It is preferred according to the invention that the linear PEI isobtained by complete or essentially complete deacylation of PEOX. Forexample, PEOX with a molecular weight of 50 kDa gives a linear PEI witha molecular weight of 22 kDa. It is preferred that at least 92%, atleast 93%, at least 94%, at least 95%, at least 96%, at least 97%, atleast 98%, at least 99%, or essentially 100% of the substituents of thenitrogen atoms in the polyalkyleneimine such as polyethyleneimine arehydrogen (i.e. R in the above formula is H). It is thus preferred thatat least 92%, at least 93%, at least 94%, at least 95%, at least 96%, atleast 97%, at least 98%, at least 99%, or essentially 100% of thenitrogen atoms in the polyalkyleneimine such as polyethyleneimine areprotonatable.

A preferred polyalkyleneimine according to the invention ispolyethylenimine (PEI), in particular linear polyethylenimine. Suchlinear polyethylenimine preferably has a molar mass between 15 kDa and30 kDa, and is preferably used in combination with self-replicating orself-amplifying RNA, where the N/P ratio is preferably between 6 and 15,and the linear polyethylenimine and the self-replicating orself-amplifying RNA are preferably present in polyplex particles havinga size of less than 200 nm, preferably less than 150 nm, and even morepreferably less than 100 nm.

In one embodiment of the invention, the polyalkyleneimine is acombination of short polyalkyleneimine, such as short polyethyleneimine,of between 0.6 and 11 kDa, preferably of between 1 and 6 kDa or between1 and 4 kDa such as between 1 and 3 kDa (either linear and/or branched)and long polyalkyleneimine, such as long polyethyleneimine, of between20 and 40 kDa (either linear and/or branched), where the total N/P ratiois preferably between 8 and 16, such as between 9 and 14, e.g., between10 and 12. In one embodiment, the N/P ratio between longpolyalkyleneimine and RNA is between 1 and 6 such as between 2 and 5such as 3 or 4.

Polyethylenimine (PEI) is an organic macromolecule with a highcationic-charge-density. PEI may compact nucleic acids into positivelycharged particles capable of interacting with anionic proteoglycans atthe cell surface and facilitating entry of the particles by endocytosis.

Several manufacturing methods exist for PEI. According to the invention,linear polyethylenimine is preferably synthesised and prepared by amethod comprising the steps of, from a determined quantity of monomer2-ethyl-2-oxazoline at a purity superior to 99%, thoroughly drying saidquantity of monomer, and polymerising said quantity of monomer forobtaining poly (2-ethyl-2-oxazoline) (PEOX) by:

-   -   after thorough drying of a predetermined quantity of        acetonitrile, using said acetonitrile as solvent in said        quantity of dried monomer, while adding a predetermined quantity        of thoroughly dried initiator of the reaction of polymerisation,        and mixing them altogether,    -   purifying said obtained PEOX by evaporation to remove said        solvent, while performing at least three times successive        washing/precipitation steps with methanol and diethyl ether and        corresponding filtrations,        said operations of drying, polymerising, and purifying being        arranged to obtain (i), by performing H NMR tests, correct        identification of said PEOX polymer, confirmation of absence of        monomer to a level <1.0% and confirmation of absence of solvent        to a level <5.0% and (ii), by performing Gel Permeation        Chromatography, a mean of molecular weight (Mw)>23,000 Da and        polydispersity (Mw/Mn) of said PEOX<1.5,    -   hydrolysing said PEOX with hydrochloric acid for obtaining said        PEI sufficiently efficiently to have, by performing ¹H-NMR        tests, an amount of residual side chains or propionic acid <5%        and to identify the PEI as a single peak.

By thoroughly drying a specific quantity of monomer, acetonitrile or theinitiator, one should understand obtaining, just before use, a reductionof the humidity below 10 ppm of water, which can be obtained by dryingon calcium hydride over 48 h and then by distillation and collecting themonomer above the temperature of 129° C.

One or more of the following features are preferred according to theinvention:

(i) the mean of molecular weight (Mw) of the PEOX is such as 40,000Da<Mw<60,000 Da;

(ii) the monomer/initiator ratio is about 500 (by about one shouldunderstand ±5%);

(iii) the monomer/initiator ratio is 480;

(iv) the monomer is at a Purity Superior to 99.95%;

(v) the initiator is mixed with the acetonitrile before addition to themonomer;

(vi) the polymerisation is performed during more than 20 hours at atemperature superior to 85° C.;

(vii) the temperature of polymerisation is superior or equal to 105° C.;

(viii) after the first filtration, the residue is washed freely with asolvent such as MeOH, and after addition of diethyl ether, the poly(2-ethyl-2-oxazoline) is naturally separated as oil from solution, theoverall solvent is decanted and said washing and separation is repeatedat least four times before drying in vacuo;

(ix) the hydrolysing step comprises removing from the reaction mixturethe discharged propionic acid obtained by azeotropic distillationregularly and during at least one day, while monitoring the process ofreaction by ¹H-NMR spectroscopy;

(x) the residue obtained at the end of the process of reaction isdiluted in water and evaporated at least three times to remove traces ofpropionic acid, then the residue is dissolved again in water andfiltered before lyophilisation;

(xi) the filtration is provided through a sterile membrane with adimension of mesh between 0.20 μm and 0.25 μm, particularly a sterilecellular acetate membrane.

Advantageously a linear PEI for use according to the invention ischaracterized in that the intermediate PEOX has a molecular weight Mwsuch as 40,000<Mw<60,000 Da.

The degree of polymerization is controlled by the monomer/initiatorratio and by the yield of synthesis. Molecular weight determination canbe performed by gel permeation chromatography (GPC).

The term “nucleic acid” according to the invention comprisesdeoxyribonucleic acid (DNA), ribonucleic acid (RNA), and locked nucleicacid (LNA). According to the invention, nucleic acids comprise genomicDNA, cDNA, mRNA, viral RNA, recombinantly prepared and chemicallysynthesized molecules. According to the invention, a nucleic acid may bein the form of a single stranded or double-stranded and linear orcovalently closed circular molecule. The term “nucleic acid” accordingto the invention also comprises a chemical derivatization of a nucleicacid on a nucleotide base, on the sugar or on the phosphate, and nucleicacids containing non-natural nucleotides and nucleotide analogs. Thenucleic acids described may be isolated and/or recombinant nucleicacids.

The term “isolated” as used herein, is intended to refer to a moleculewhich is substantially free of other molecules such as other cellularmaterial. The term “isolated nucleic acid” means according to theinvention that the nucleic acid has been (i) amplified in vitro, forexample by polymerase chain reaction (PCR), (ii) recombinantly producedby cloning, (iii) purified, for example by cleavage andgel-electrophoretic fractionation, or (iv) synthesized, for example bychemical synthesis. An isolated nucleic acid is a nucleic acid availableto manipulation by recombinant techniques.

The term “recombinant” in the context of the present invention means“made through genetic engineering”. Preferably, a “recombinant object”in the context of the present invention is not occurring naturally.

The term “naturally occurring” as used herein refers to the fact that anobject can be found in nature. For example, a peptide or nucleic acidthat is present in an organism (including viruses) and can be isolatedfrom a source in nature and which has not been intentionally modified byman in the laboratory is naturally occurring. The term “found in nature”means “present in nature” and includes known objects as well as objectsthat have not yet been discovered and/or isolated from nature, but thatmay be discovered and/or isolated in the future from a natural source.

According to the invention “nucleic acid sequence” refers to thesequence of nucleotides in a nucleic acid, e.g. a ribonucleic acid (RNA)or a deoxyribonucleic acid (DNA). The term may refer to an entirenucleic acid molecule (such as to the single strand of an entire nucleicacid molecule) or to a part (e.g. a fragment) thereof.

“3′ end of a nucleic acid” refers according to the invention to that endwhich has a free hydroxy group. In a diagrammatic representation ofdouble-stranded nucleic acids, in particular DNA, the 3′ end is alwayson the right-hand side. “5′ end of a nucleic acid” refers according tothe invention to that end which has a free phosphate group. In adiagrammatic representation of double-strand nucleic acids, inparticular DNA, the 5′ end is always on the left-hand side.

5′ end 5′--P-NNNNNNN-OH-3′ 3′ end 3′-HO-NNNNNNN-P--5'

“Upstream” describes the relative positioning of a first element of anucleic acid molecule with respect to a second element of that nucleicacid molecule, wherein both elements are comprised in the same nucleicacid molecule, and wherein the first element is located nearer to the 5′end of the nucleic acid molecule than the second element of that nucleicacid molecule. The second element is then said to be “downstream” of thefirst element of that nucleic acid molecule. An element that is located“upstream” of a second element can be synonymously referred to as beinglocated “5′” of that second element. For a double-stranded nucleic acidmolecule, indications like “upstream” and “downstream” are given withrespect to the (+) strand.

According to the invention, the term “gene” refers to a particularnucleic acid sequence which is responsible for producing one or morecellular products and/or for achieving one or more intercellular orintracellular functions. More specifically, said term relates to anucleic acid section (DNA or RNA) which comprises a nucleic acid codingfor a specific protein or a functional or structural RNA molecule.

The term “vector” is used here in its most general meaning and comprisesany intermediate vehicles for a nucleic acid which, for example, enablesaid nucleic acid to be introduced into prokaryotic and/or eukaryotichost cells and, where appropriate, to be integrated into a genome. Suchvectors are preferably replicated and/or expressed in the cell. Vectorscomprise plasmids, phagemids, virus genomes, and fractions thereof.

In the context of the present invention, the term “RNA” relates to amolecule which comprises ribonucleotide residues and preferably beingentirely or substantially composed of ribonucleotide residues andcomprises all RNA types described herein. The term “ribonucleotide”relates to a nucleotide with a hydroxyl group at the 2′-position of aβ-D-ribofuranosyl group. The term “RNA” comprises double-stranded RNA,single stranded RNA, isolated RNA such as partially or completelypurified RNA, essentially pure RNA, synthetic RNA, and recombinantlygenerated RNA such as modified RNA which differs from naturallyoccurring RNA by addition, deletion, substitution and/or alteration ofone or more nucleotides. Such alterations can include addition ofnon-nucleotide material, such as to the end(s) of a RNA or internally,for example at one or more nucleotides of the RNA. Nucleotides in RNAmolecules can also comprise non-standard nucleotides, such asnon-naturally occurring nucleotides or chemically synthesizednucleotides or deoxynucleotides. These altered RNAs can be referred toas analogs, particularly analogs of naturally-occurring RNAs. The RNAused according to the present invention may have a known composition, orthe composition of the RNA may be partially or entirely unknown.

The term “stability” of RNA relates to the “half-life” of RNA.“Half-life” relates to the period of time which is needed to eliminatehalf of the activity, amount, or number of molecules. In the context ofthe present invention, the half-life of an RNA is indicative for thestability of said RNA. The half-life of RNA may influence the “durationof expression” of the RNA. It can be expected that RNA having a longhalf-life will be expressed for an extended time period.

The term “translation efficiency” relates to the amount of translationproduct provided by an RNA molecule within a particular period of time.

According to the invention, “double-stranded RNA” or “dsRNA” means RNAwith two partially or completely complementary strands.

According to the invention, RNA is preferably single stranded RNA(ssRNA). The term “single stranded RNA” generally refers to an RNAmolecule to which no complementary nucleic acid molecule (typically nocomplementary RNA molecule) is associated. Single stranded RNA maycontain self-complementary sequences that allow parts of the RNA to foldback and to form secondary structure motifs including without limitationbase pairs, stems, stem loops and bulges. Single stranded RNA can existas minus strand [(−) strand] or as plus strand [(+) strand]. The (+)strand is the strand that comprises or encodes genetic information. Thegenetic information may be for example a polynucleotide sequenceencoding a protein. When the (+) strand RNA encodes a protein, the (+)strand may serve directly as template for translation (proteinsynthesis). The (−) strand is the complement of the (+) strand. In thecase of double-stranded RNA, (+) strand and (−) strand are two separateRNA molecules, and both these RNA molecules associate with each other toform a double-stranded RNA (“duplex RNA”).

Particularly preferred single stranded RNA according to the invention ismRNA and replicon-RNA such as self-replicating RNA. According to thepresent invention, the RNA can be coding RNA, i.e. RNA encoding apeptide or protein. Preferably, the RNA is pharmaceutically active RNA.

A “pharmaceutically active RNA” is a RNA that encodes a pharmaceuticallyactive peptide or protein such as an antigen or an immunologicallyactive compound (which does not encode an antigen) or ispharmaceutically active in its own, e.g., it has one or morepharmaceutical activities such as those described for pharmaceuticallyactive proteins.

According to the invention, the term “RNA encoding a peptide or protein”means that the RNA, if present in the appropriate environment,preferably within a cell, can direct the assembly of amino acids toproduce the peptide or protein during the process of translation.Preferably, coding RNA according to the invention is able to interactwith the cellular translation machinery allowing translation of thecoding RNA to yield a peptide or protein.

According to the invention, the term “mRNA” means “messenger-RNA” andrelates to a transcript which is typically generated by using a DNAtemplate and encodes a peptide or protein. Typically, mRNA comprises a5′-UTR, a protein coding region, a 3′-UTR, and a poly(A) sequence. mRNAmay be generated by in vitro transcription from a DNA template. The invitro transcription methodology is known to the skilled person. Forexample, there is a variety of in vitro transcription kits commerciallyavailable. According to the invention, mRNA may be modified bystabilizing modifications and capping.

The term “untranslated region” or “UTR” relates to a region in a DNAmolecule which is transcribed but is not translated into an amino acidsequence, or to the corresponding region in an RNA molecule, such as anmRNA molecule. An untranslated region (UTR) can be present 5′ (upstream)of an open reading frame (5′-UTR) and/or 3′ (downstream) of an openreading frame (3′-UTR).

A 3′-UTR, if present, is located at the 3′ end of a gene, downstream ofthe termination codon of a protein-encoding region, but the term“3′-UTR” does preferably not include the poly(A) tail. Thus, the 3′-UTRis upstream of the poly(A) tail (if present), e.g. directly adjacent tothe poly(A) tail. A 5′-UTR, if present, is located at the 5′ end of agene, upstream of the start codon of a protein-encoding region. A 5′-UTRis downstream of the 5′-cap (if present), e.g. directly adjacent to the5′-cap. 5′- and/or 3-untranslated regions may, according to theinvention, be functionally linked to an open reading frame, so as forthese regions to be associated with the open reading frame in such a waythat the stability and/or translation efficiency of the RNA comprisingsaid open reading frame are increased.

According to the invention, the terms “poly(A) sequence” or “poly(A)tail” refer to an uninterrupted or interrupted sequence of adenylateresidues which is typically located at the 3′ end of an RNA molecule. Anuninterrupted sequence is characterized by consecutive adenylateresidues. In nature, an uninterrupted poly(A) sequence is typical. Whilea poly(A) sequence is normally not encoded in eukaryotic DNA, but isattached during eukaryotic transcription in the cell nucleus to the free3′ end of the RNA by a template-independent RNA polymerase aftertranscription, the present invention encompasses poly(A) sequencesencoded by DNA.

Terms such as “5′-cap”, “cap”, “5′-cap structure”, or “cap structure”are used synonymously to refer to a dinucleotide that is found on the 5′end of some eukaryotic primary transcripts such as precursor messengerRNA. A 5′-cap is a structure wherein a (optionally modified) guanosineis bonded to the first nucleotide of an mRNA molecule via a 5′ to 5′triphosphate linkage (or modified triphosphate linkage in the case ofcertain cap analogs). The terms can refer to a conventional cap or to acap analog.

RNA molecules according to the invention may be characterized by a5′-cap, a 5′-UTR, a 3′-UTR, a poly(A) sequence, and/or adaptation of thecodon usage.

RNA molecules for use according to the invention preferably have a sizeof more than 2000 bases, preferably more than 3000 bases, more than 4000bases, more than 5000 bases, more than 6000 bases, more than 7000 bases,more than 8000 bases, more than 9000 bases, or more than 10000 bases.RNA molecules for use according to the invention preferably have a sizeof 6000 to 20000 bases, preferably 6000 to 15000 bases, preferably 9000to 12000 bases.

According to the invention, the term “expression” is used in its mostgeneral meaning and comprises production of RNA and/or protein. It alsocomprises partial expression of nucleic acids. Furthermore, expressionmay be transient or stable. With respect to RNA, the term “expression”or “translation” relates to the process in the ribosomes of a cell bywhich a strand of coding RNA (e.g. messenger RNA) directs the assemblyof a sequence of amino acids to make a peptide or protein.

The terms “transcription” and “transcribing” relate to a process duringwhich a nucleic acid molecule with a particular nucleic acid sequence(the “nucleic acid template”) is read by an RNA polymerase so that theRNA polymerase produces a single stranded RNA molecule. Duringtranscription, the genetic information in a nucleic acid template istranscribed. The nucleic acid template may be DNA; however, e.g. in thecase of transcription from an alphaviral nucleic acid template, thetemplate is typically RNA. Subsequently, the transcribed RNA may betranslated into protein. According to the present invention, the term“transcription” comprises “in vitro transcription”, wherein the term “invitro transcription” relates to a process wherein RNA, in particularmRNA, is in vitro synthesized in a cell-free system. Preferably, cloningvectors are applied for the generation of transcripts. These cloningvectors are generally designated as transcription vectors and areaccording to the present invention encompassed by the term “vector”. Thecloning vectors are preferably plasmids. According to the presentinvention, RNA preferably is in vitro transcribed RNA (IVT-RNA) and maybe obtained by in vitro transcription of an appropriate DNA template.The promoter for controlling transcription can be any promoter for anyRNA polymerase. A DNA template for in vitro transcription may beobtained by cloning of a nucleic acid, in particular cDNA, andintroducing it into an appropriate vector for in vitro transcription.The cDNA may be obtained by reverse transcription of RNA.

The single stranded nucleic acid molecule produced during transcriptiontypically has a nucleic acid sequence that is the complementary sequenceof the template.

According to the invention, the terms “template” or “nucleic acidtemplate” or “template nucleic acid” generally refer to a nucleic acidsequence that may be replicated or transcribed.

The term “expression control sequence” comprises according to theinvention promoters, ribosome-binding sequences and other controlelements which control transcription of a gene or translation of thederived RNA. In particular embodiments of the invention, the expressioncontrol sequences can be regulated. The precise structure of expressioncontrol sequences may vary depending on the species or cell type butusually includes 5′-untranscribed and 5′- and 3′-untranslated sequencesinvolved in initiating transcription and translation, respectively. Morespecifically, 5′-untranscribed expression control sequences include apromoter region which encompasses a promoter sequence for transcriptioncontrol of the functionally linked gene. Expression control sequencesmay also include enhancer sequences or upstream activator sequences. Anexpression control sequence of a DNA molecule usually includes5′-untranscribed and 5′- and 3′-untranslated sequences such as TATA box,capping sequence, CAAT sequence and the like. An expression controlsequence of alphaviral RNA may include a subgenomic promoter and/or oneor more conserved sequence element(s). A specific expression controlsequence according to the present invention is a subgenomic promoter ofan alphavirus, as described herein.

The term “promoter” or “promoter region” refers to a nucleic acidsequence which controls synthesis of a transcript, e.g. a transcriptcomprising a coding sequence, by providing a recognition and bindingsite for RNA polymerase. The promoter region may include furtherrecognition or binding sites for further factors involved in regulatingtranscription of said gene. A promoter may control transcription of aprokaryotic or eukaryotic gene. A promoter may be “inducible” andinitiate transcription in response to an inducer, or may be“constitutive” if transcription is not controlled by an inducer. Aninducible promoter is expressed only to a very small extent or not atall, if an inducer is absent. In the presence of the inducer, the geneis “switched on” or the level of transcription is increased. This isusually mediated by binding of a specific transcription factor. Aspecific promoter according to the present invention is a subgenomicpromoter of an alphavirus, as described herein. Other specific promotersare genomic plus-strand or negative-strand promoters of an alphavirus.

The term “core promoter” refers to a nucleic acid sequence that iscomprised by the promoter. The core promoter is typically the minimalportion of the promoter required to properly initiate transcription. Thecore promoter typically includes the transcription start site and abinding site for RNA polymerase.

The nucleic acid sequences specified herein, in particular transcribableand coding nucleic acid sequences, may be combined with any expressioncontrol sequences which may be homologous or heterologous to saidnucleic acid sequences, with the term “homologous” referring to the factthat a nucleic acid sequence is also functionally linked naturally tothe expression control sequence, and the term “heterologous” referringto the fact that a nucleic acid sequence is not naturally functionallylinked to the expression control sequence.

A nucleic acid sequence, in particular a nucleic acid sequence codingfor a peptide or protein, and an expression control sequence are“functionally” linked to one another, if they are covalently linked toone another in such a way that transcription or expression of thetranscribable and/or coding nucleic acid sequence is under the controlor under the influence of the expression control sequence.

According to the invention, “functional linkage” or “functionallylinked” relates to a connection within a functional relationship. Anucleic acid is “functionally linked” if it is functionally related toanother nucleic acid sequence. For example, a promoter is functionallylinked to a coding sequence if it influences transcription of saidcoding sequence. Functionally linked nucleic acids are typicallyadjacent to one another, where appropriate separated by further nucleicacid sequences.

In particular embodiments, a nucleic acid is functionally linkedaccording to the invention to expression control sequences which may behomologous or heterologous with respect to the nucleic acid.

A “polymerase” generally refers to a molecular entity capable ofcatalyzing the synthesis of a polymeric molecule from monomeric buildingblocks. A “RNA polymerase” is a molecular entity capable of catalyzingthe synthesis of a RNA molecule from ribonucleotide building blocks. A“DNA polymerase” is a molecular entity capable of catalyzing thesynthesis of a DNA molecule from deoxy ribonucleotide building blocks.For the case of DNA polymerases and RNA polymerases, the molecularentity is typically a protein or an assembly or complex of multipleproteins. Typically, a DNA polymerase synthesizes a DNA molecule basedon a template nucleic acid, which is typically a DNA molecule.Typically, a RNA polymerase synthesizes a RNA molecule based on atemplate nucleic acid, which is either a DNA molecule (in that case theRNA polymerase is a DNA-dependent RNA polymerase, DdRP), or is a RNAmolecule (in that case the RNA polymerase is a RNA-dependent RNApolymerase, RdRP).

A “RNA-dependent RNA polymerase” or “RdRP”, is an enzyme that catalyzesthe transcription of RNA from an RNA template. In the case of alphaviralRNA-dependent RNA polymerase, sequential synthesis of (−) strandcomplement of genomic RNA and of (+) strand genomic RNA leads to RNAreplication. Alphaviral RNA-dependent RNA polymerase is thussynonymously referred to as “RNA replicase”. In nature, RNA-dependentRNA polymerases are typically encoded by all RNA viruses exceptretroviruses. Typical representatives of viruses encoding aRNA-dependent RNA polymerase are alphaviruses.

According to the present invention, “RNA replication” generally refersto an RNA molecule synthesized based on the nucleotide sequence of agiven RNA molecule (template RNA molecule). The RNA molecule that issynthesized may be e.g. identical or complementary to the template RNAmolecule. In general, RNA replication may occur via synthesis of a DNAintermediate, or may occur directly by RNA-dependent RNA replicationmediated by a RNA-dependent RNA polymerase (RdRP). In the case ofalphaviruses, RNA replication does not occur via a DNA intermediate, butis mediated by a RNA-dependent RNA polymerase (RdRP): a template RNAstrand (first RNA strand)—or a part thereof—serves as template for thesynthesis of a second RNA strand that is complementary to the first RNAstrand or to a part thereof. The second RNA strand—or a part thereof—mayin turn optionally serve as a template for synthesis of a third RNAstrand that is complementary to the second RNA strand or to a partthereof. Thereby, the third RNA strand is identical to the first RNAstrand or to a part thereof. Thus, RNA-dependent RNA polymerase iscapable of directly synthesizing a complementary RNA strand of atemplate, and of indirectly synthesizing an identical RNA strand (via acomplementary intermediate strand).

According to the invention, the term “template RNA” refers to RNA thatcan be transcribed or replicated by an RNA-dependent RNA polymerase.

In a preferred embodiment of the invention, the RNA used according tothe invention is replicon RNA or simply “a replicon”, in particularself-replicating RNA. In one particularly preferred embodiment, thereplicon or self-replicating RNA is derived from or comprises elementsderived from a ssRNA virus, in particular a positive-stranded ssRNAvirus such as an alphavirus.

In general, RNA viruses are a diverse group of infectious particles withan RNA genome. RNA viruses can be sub-grouped into single stranded RNA(ssRNA) and double-stranded RNA (dsRNA) viruses, and the ssRNA virusescan be further generally divided into positive-stranded [(+) stranded]and/or negative-stranded [(−) stranded] viruses. Positive-stranded RNAviruses are prima facie attractive as a delivery system in biomedicinebecause their RNA may serve directly as template for translation in thehost cell.

Alphaviruses are typical representatives of positive-stranded RNAviruses. The hosts of alphaviruses include a wide range of organisms,comprising insects, fish and mammals, such as domesticated animals andhumans. Alphaviruses replicate in the cytoplasm of infected cells (forreview of the alphaviral life cycle see José et al., Future Microbiol.,2009, vol. 4, pp. 837-856). The total genome length of many alphavirusestypically ranges between 11,000 and 12,000 nucleotides, and the genomicRNA typically has a 5′-cap, and a 3′ poly(A) tail. The genome ofalphaviruses encodes non-structural proteins (involved in transcription,modification and replication of viral RNA and in protein modification)and structural proteins (forming the virus particle). There aretypically two open reading frames (ORFs) in the genome.

The four non-structural proteins (nsP1-nsP4) are typically encodedtogether by a first ORF beginning near the 5′ terminus of the genome,while alphavirus structural proteins are encoded together by a secondORF which is found downstream of the first ORF and extends near the 3′terminus of the genome. Typically, the first ORF is larger than thesecond ORF, the ratio being roughly 2:1.

In cells infected by an alphavirus, only the nucleic acid sequenceencoding non-structural proteins is translated from the genomic RNA,while the genetic information encoding structural proteins istranslatable from a subgenomic transcript, which is an RNA molecule thatresembles eukaryotic messenger RNA (mRNA; Gould et al., 2010, AntiviralRes., vol. 87 pp. 111-124). Following infection, i.e. at early stages ofthe viral life cycle, the (+) stranded genomic RNA directly acts like amessenger RNA for the translation of the open reading frame encoding thenon-structural poly-protein (nsP1234). In some alphaviruses, there is anopal stop codon between the coding sequences of nsP3 and nsP4:polyprotein P123, containing nsP1, nsP2, and nsP3, is produced whentranslation terminates at the opal stop codon, and polyprotein P1234,containing in addition nsP4, is produced upon readthrough of this opalcodon (Strauss & Strauss, Microbiol. Rev., 1994, vol. 58, pp. 491-562;Rupp et al., 2015, J. Gen. Virology, vol. 96, pp. 2483-2500). nsP1234 isautoproteolytically cleaved into the fragments nsP123 and nsP4. Thepolypeptides nsP123 and nsP4 associate to form the (−) strand replicasecomplex that transcribes (−) stranded RNA, using the (+) strandedgenomic RNA as template. Typically at later stages, the nsP123 fragmentis completely cleaved into individual proteins nsP1, nsP2 and nsP3(Shirako & Strauss, 1994, J. Virol., vol. 68, pp. 1874-1885). All fourproteins form the (+) strand replicase complex that synthesizes new (+)stranded genomes, using the (−) stranded complement of genomic RNA astemplate (Kim et al., 2004, Virology, vol. 323, pp. 153-163, Vasiljevaet al., 2003, J. Biol. Chem. vol. 278, pp. 41636-41645).

In infected cells, subgenomic RNA as well as new genomic RNA is providedwith a 5′-cap by nsP1 (Pettersson et al. 1980, Eur. J. Biochem. 105,435-443; Rozanov et al., 1992, J. Gen. Virology, vol. 73, pp.2129-2134), and provided with a poly-adenylate [poly(A)] tail by nsP4(Rubach et al., Virology, 2009, vol. 384, pp. 201-208). Thus, bothsubgenomic RNA and genomic RNA resemble messenger RNA (mRNA).

Alphavirus structural proteins are typically encoded by one single openreading frame under control of a subgenomic promoter (Strauss & Strauss,Microbiol. Rev., 1994, vol. 58, pp. 491-562). The subgenomic promoter isrecognized by alphaviral non-structural proteins acting in cis. Inparticular, alphavirus replicase synthesizes a (+) stranded subgenomictranscript using the (−) stranded complement of genomic RNA as template.The (+) stranded subgenomic transcript encodes the alphavirus structuralproteins (Kim et al., 2004, Virology, vol. 323, pp. 153-163, Vasiljevaet al., 2003, J. Biol. Chem. vol. 278, pp. 41636-41645). The subgenomicRNA transcript serves as template for translation of the open readingframe encoding the structural proteins as one poly-protein, and thepoly-protein is cleaved to yield the structural proteins. At a latestage of alphavirus infection in a host cell, a packaging signal whichis located within the coding sequence of nsP2 ensures selectivepackaging of genomic RNA into budding virions, packaged by structuralproteins (White et al., 1998, J. Virol., vol. 72, pp. 4320-4326).

In infected cells, (−) strand RNA synthesis is typically observed onlyin the first 3-4 h post infection, and is undetectable at late stages,at which time the synthesis of only (+) strand RNA (both genomic andsubgenomic) is observed. According to Frolov et al., 2001, RNA, vol. 7,pp. 1638-1651, the prevailing model for regulation of RNA synthesissuggests a dependence on the processing of the non-structuralpoly-protein: initial cleavage of the non-structural polyprotein nsP1234yields nsP123 and nsP4; nsP4 acts as RNA-dependent RNA polymerase (RdRp)that is active for (−) strand synthesis, but inefficient for thegeneration of (+) strand RNAs. Further processing of the polyproteinnsP123, including cleavage at the nsP2/nsP3 junction, changes thetemplate specificity of the replicase to increase synthesis of (+)strand RNA and to decrease or terminate synthesis of (−) strand RNA.

The synthesis of alphaviral RNA is also regulated by cis-acting RNAelements, including four conserved sequence elements (CSEs; Strauss &Strauss, Microbiol. Rev., 1994, vol. 58, pp. 491-562; and Frolov, 2001,RNA, vol. 7, pp. 1638-1651).

In general, the 5′ replication recognition sequence of the alphavirusgenome is characterized by low overall homology between differentalphaviruses, but has a conserved predicted secondary structure. The 5′replication recognition sequence of the alphavirus genome is not onlyinvolved in translation initiation, but also comprises the 5′replication recognition sequence comprising two conserved sequenceelements involved in synthesis of viral RNA, CSE 1 and CSE 2. For thefunction of CSE 1 and 2, the secondary structure is believed to be moreimportant than the linear sequence (Strauss & Strauss, Microbiol. Rev.,1994, vol. 58, pp. 491-562).

In contrast, the 3′ terminal sequence of the alphavirus genome, i.e. thesequence immediately upstream of the poly(A) sequence, is characterizedby a conserved primary structure, particularly by conserved sequenceelement 4 (CSE 4), also termed “19-nt conserved sequence”, which isimportant for initiation of (−) strand synthesis.

CSE 3, also termed “junction sequence” is a conserved sequence elementon the (+) strand of alphaviral genomic RNA, and the complement of CSE 3on the (−) strand acts as promoter for subgenomic RNA transcription(Strauss & Strauss, Microbiol. Rev., 1994, vol. 58, pp. 491-562; Frolovet al., 2001, RNA, vol. 7, pp. 1638-1651). CSE 3 typically overlaps withthe region encoding the C-terminal fragment of nsP4.

In addition to alphavirus proteins, also host cell factors, presumablyproteins, may bind to conserved sequence elements (Strauss & Strauss,supra).

Alphavirus-derived vectors have been proposed for delivery of foreigngenetic information into target cells or target organisms. In simpleapproaches, the open reading frame encoding alphaviral structuralproteins is replaced by an open reading frame encoding a protein ofinterest. Alphavirus-based trans-replication systems rely on alphavirusnucleotide sequence elements on two separate nucleic acid molecules: onenucleic acid molecule encodes a viral replicase (typically aspoly-protein nsP1234), and the other nucleic acid molecule is capable ofbeing replicated by said replicase in trans (hence the designationtrans-replication system). trans-replication requires the presence ofboth these nucleic acid molecules in a given host cell. The nucleic acidmolecule capable of being replicated by the replicase in trans mustcomprise certain alphaviral sequence elements to allow recognition andRNA synthesis by the alphaviral replicase.

According to the invention, the term “alphavirus” is to be understoodbroadly and includes any virus particle that has characteristics ofalphaviruses. Characteristics of alphavirus include the presence of a(+) stranded RNA which encodes genetic information suitable forreplication in a host cell, including RNA polymerase activity. Furthercharacteristics of many alphaviruses are described e.g. in Strauss &Strauss, Microbiol. Rev., 1994, vol. 58, pp. 491-562. The term“alphavirus” includes alphavirus found in nature, as well as any variantor derivative thereof. In some embodiments, a variant or derivative isnot found in nature.

In one embodiment, the alphavirus is an alphavirus found in nature.Typically, an alphavirus found in nature is infectious to any one ormore eukaryotic organisms, such as an animal (including a vertebratesuch as a human, and an arthropod such as an insect).

An alphavirus found in nature is preferably selected from the groupconsisting of the following: Barmah Forest virus complex (comprisingBarmah Forest virus); Eastern equine encephalitis complex (comprisingseven antigenic types of Eastern equine encephalitis virus); Middelburgvirus complex (comprising Middelburg virus); Ndumu virus complex(comprising Ndumu virus); Semliki Forest virus complex (comprisingBebaru virus, Chikungunya virus, Mayaro virus and its subtype Una virus,O'Nyong Nyong virus, and its subtype Igbo-Ora virus, Ross River virusand its subtypes Bebaru virus, Getah virus, Sagiyama virus, SemlikiForest virus and its subtype Me Tri virus); Venezuelan equineencephalitis complex (comprising Cabassou virus, Everglades virus, Mossodas Pedras virus, Mucambo virus, Paramana virus, Pixuna virus, Rio Negrovirus, Trocara virus and its subtype Bijou Bridge virus, Venezuelanequine encephalitis virus); Western equine encephalitis complex(comprising Aura virus, Babanki virus, Kyzylagach virus, Sindbis virus,Ockelbo virus, Whataroa virus, Buggy Creek virus, Fort Morgan virus,Highlands J virus, Western equine encephalitis virus); and someunclassified viruses including Salmon pancreatic disease virus; SleepingDisease virus; Southern elephant seal virus; Tonate virus. Morepreferably, the alphavirus is selected from the group consisting ofSemliki Forest virus complex (comprising the virus types as indicatedabove, including Semliki Forest virus), Western equine encephalitiscomplex (comprising the virus types as indicated above, includingSindbis virus), Eastern equine encephalitis virus (comprising the virustypes as indicated above), Venezuelan equine encephalitis complex(comprising the virus types as indicated above, including Venezuelanequine encephalitis virus).

In a further preferred embodiment, the alphavirus is Semliki Forestvirus. In an alternative further preferred embodiment, the alphavirus isSindbis virus. In an alternative further preferred embodiment, thealphavirus is Venezuelan equine encephalitis virus.

In some embodiments of the present invention, the alphavirus is not analphavirus found in nature. Typically, an alphavirus not found in natureis a variant or derivative of an alphavirus found in nature, that isdistinguished from an alphavirus found in nature by at least onemutation in the nucleotide sequence, i.e. the genomic RNA. The mutationin the nucleotide sequence may be selected from an insertion, asubstitution or a deletion of one or more nucleotides, compared to analphavirus found in nature. A mutation in the nucleotide sequence may ormay not be associated with a mutation in a polypeptide or proteinencoded by the nucleotide sequence. For example, an alphavirus not foundin nature may be an attenuated alphavirus. An attenuated alphavirus notfound in nature is an alphavirus that typically has at least onemutation in its nucleotide sequence by which it is distinguished from analphavirus found in nature, and that is either not infectious at all, orthat is infectious but has a lower disease-producing ability or nodisease-producing ability at all. As an illustrative example, TC83 is anattenuated alphavirus that is distinguished from the Venezuelan equineencephalitis virus (VEEV) found in nature (McKinney et al., 1963, Am. J.Trop. Med. Hyg., 1963, vol. 12; pp. 597-603).

Members of the alphavirus genus may also be classified based on theirrelative clinical features in humans: alphaviruses associated primarilywith encephalitis, and alphaviruses associated primarily with fever,rash, and polyarthritis.

The term “alphaviral” means found in an alphavirus, or originating froman alphavirus or derived from an alphavirus, e.g. by geneticengineering.

According to the invention, “SFV” stands for Semliki Forest virus.According to the invention, “SIN” or “SINV” stands for Sindbis virus.According to the invention, “VEE” or “VEEV” stands for Venezuelan equineencephalitis virus.

According to the invention, the term “of an alphavirus” or “derived froman alphavirus” refers to an entity of origin from an alphavirus. Forillustration, a protein of an alphavirus may refer to a protein that isfound in alphavirus and/or to a protein that is encoded by alphavirus;and a nucleic acid sequence of an alphavirus may refer to a nucleic acidsequence that is found in alphavirus and/or to a nucleic acid sequencethat is encoded by alphavirus. Preferably, a nucleic acid sequence “ofan alphavirus” refers to a nucleic acid sequence “of the genome of analphavirus” and/or “of genomic RNA of an alphavirus”.

According to the invention, the term “alphaviral RNA” refers to any oneor more of alphaviral genomic RNA (i.e. (+) strand), complement ofalphaviral genomic RNA (i.e. (−) strand), and the subgenomic transcript(i.e. (+) strand), or a fragment of any thereof.

According to the invention, “alphavirus genome” refers to genomic (+)strand RNA of an alphavirus.

According to the invention, the term “native alphavirus sequence” andsimilar terms typically refer to a (e.g. nucleic acid) sequence of anaturally occurring alphavirus (alphavirus found in nature). In someembodiments, the term “native alphavirus sequence” also includes asequence of an attenuated alphavirus.

According to the invention, the term “5′ replication recognitionsequence” preferably refers to a continuous nucleic acid sequence,preferably a ribonucleic acid sequence, that is identical or homologousto a 5′ fragment of the alphavirus genome. The “5′ replicationrecognition sequence” is a nucleic acid sequence that can be recognizedby an alphaviral replicase. The term 5′ replication recognition sequenceincludes native 5′ replication recognition sequences as well asfunctional equivalents thereof, such as, e.g., functional variants of a5′ replication recognition sequence of alphavirus found in nature. The5′ replication recognition sequence is required for synthesis of the (−)strand complement of alphavirus genomic RNA, and is required forsynthesis of (+) strand viral genomic RNA based on a (−) strandtemplate. A native 5′ replication recognition sequence typically encodesat least the N-terminal fragment of nsP1; but does not comprise theentire open reading frame encoding nsP1234. In view of the fact that anative 5′ replication recognition sequence typically encodes at leastthe N-terminal fragment of nsP1, a native 5′ replication recognitionsequence typically comprises at least one initiation codon, typicallyAUG. In one embodiment, the 5′ replication recognition sequencecomprises conserved sequence element 1 of an alphavirus genome (CSE 1)or a variant thereof and conserved sequence element 2 of an alphavirusgenome (CSE 2) or a variant thereof. The 5′ replication recognitionsequence is typically capable of forming four stem loops (SL), i.e. SL1,SL2, SL3, SL4. The numbering of these stem loops begins at the 5′ end ofthe 5′ replication recognition sequence.

According to the invention, the term “3′ replication recognitionsequence” preferably refers to a continuous nucleic acid sequence,preferably a ribonucleic acid sequence, that is identical or homologousto a 3′ fragment of the alphavirus genome. The “3′ replicationrecognition sequence” is a nucleic acid sequence that can be recognizedby an alphaviral replicase. The term 3′ replication recognition sequenceincludes native 3′ replication recognition sequences as well asfunctional equivalents thereof, such as, e.g., functional variants of a3′ replication recognition sequence of alphavirus found in nature. The3′ replication recognition sequence is required for synthesis of the (−)strand complement of alphavirus genomic RNA. In one embodiment, the 3′replication recognition sequence comprises conserved sequence element 4of an alphavirus genome (CSE 4) or a variant thereof and optionally thepoly(A) tail of an alphavirus genome.

The term “conserved sequence element” or “CSE” refers to a nucleotidesequence found in alphavirus RNA. These sequence elements are termed“conserved” because orthologs are present in the genome of differentalphaviruses, and orthologous CSEs of different alphaviruses preferablyshare a high percentage of sequence identity and/or a similar secondaryor tertiary structure. The term CSE includes CSE 1, CSE 2, CSE 3 and CSE4.

According to the invention, the terms “CSE 1” or “44-nt CSE”synonymously refer to a nucleotide sequence that is required for (+)strand synthesis from a (−) strand template. The term “CSE 1” refers toa sequence on the (+) strand; and the complementary sequence of CSE 1(on the (−) strand) functions as a promoter for (+) strand synthesis.Preferably, the term CSE 1 includes the most 5′ nucleotide of thealphavirus genome. CSE 1 typically forms a conserved stem-loopstructure. Without wishing to be bound to a particular theory, it isbelieved that, for CSE 1, the secondary structure is more important thanthe primary structure, i.e. the linear sequence. In genomic RNA of themodel alphavirus Sindbis virus, CSE 1 consists of a consecutive sequenceof 44 nucleotides, which is formed by the most 5′ 44 nucleotides of thegenomic RNA (Strauss & Strauss, Microbiol. Rev., 1994, vol. 58, pp.491-562).

According to the invention, the terms “CSE 2” or “51-nt CSE”synonymously refer to a nucleotide sequence that is required for (−)strand synthesis from a (+) strand template. The (+) strand template istypically alphavirus genomic RNA or an RNA replicon (note that thesubgenomic RNA transcript, which does not comprise CSE 2, does notfunction as a template for (−) strand synthesis). In alphavirus genomicRNA, CSE 2 is typically localized within the coding sequence for nsP1.In genomic RNA of the model alphavirus Sindbis virus, the 51-nt CSE islocated at nucleotide positions 155-205 of genomic RNA (Frolov et al.,2001, RNA, vol. 7, pp. 1638-1651). CSE 2 forms typically two conservedstem loop structures. These stem loop structures are designated as stemloop 3 (SL3) and stem loop 4 (SL4) because they are the third and fourthconserved stem loop, respectively, of alphavirus genomic RNA, countedfrom the 5′ end of alphavirus genomic RNA. Without wishing to be boundto a particular theory, it is believed that, for CSE 2, the secondarystructure is more important than the primary structure, i.e. the linearsequence.

According to the invention, the terms “CSE 3” or “junction sequence”synonymously refer to a nucleotide sequence that is derived fromalphaviral genomic RNA and that comprises the start site of thesubgenomic RNA. The complement of this sequence in the (−) strand actsto promote subgenomic RNA transcription. In alphavirus genomic RNA, CSE3 typically overlaps with the region encoding the C-terminal fragment ofnsP4 and extends to a short non-coding region located upstream of theopen reading frame encoding the structural proteins.

According to the invention, the terms “CSE 4” or “19-nt conservedsequence” or “19-nt CSE” synonymously refer to a nucleotide sequencefrom alphaviral genomic RNA, immediately upstream of the poly(A)sequence in the 3′ untranslated region of the alphavirus genome. CSE 4typically consists of 19 consecutive nucleotides. Without wishing to bebound to a particular theory, CSE 4 is understood to function as a corepromoter for initiation of (−) strand synthesis (José et al., FutureMicrobiol., 2009, vol. 4, pp. 837-856); and/or CSE 4 and the poly(A)tail of the alphavirus genomic RNA are understood to function togetherfor efficient (−) strand synthesis (Hardy & Rice, J. Virol., 2005, vol.79, pp. 4630-4639).

According to the invention, the term “subgenomic promoter” or “SGP”refers to a nucleic acid sequence upstream (5′) of a nucleic acidsequence (e.g. coding sequence), which controls transcription of saidnucleic acid sequence by providing a recognition and binding site forRNA polymerase, typically RNA-dependent RNA polymerase, in particularfunctional alphavirus non-structural protein. The SGP may includefurther recognition or binding sites for further factors. A subgenomicpromoter is typically a genetic element of a positive strand RNA virus,such as an alphavirus. A subgenomic promoter of alphavirus is a nucleicacid sequence comprised in the viral genomic RNA. The subgenomicpromoter is generally characterized in that it allows initiation of thetranscription (RNA synthesis) in the presence of an RNA-dependent RNApolymerase, e.g. functional alphavirus non-structural protein. A RNA (−)strand, i.e. the complement of alphaviral genomic RNA, serves as atemplate for synthesis of a (+) strand subgenomic transcript, andsynthesis of the (+) strand subgenomic transcript is typically initiatedat or near the subgenomic promoter. The term “subgenomic promoter” asused herein, is not confined to any particular localization in a nucleicacid comprising such subgenomic promoter. In some embodiments, the SGPis identical to CSE 3 or overlaps with CSE 3 or comprises CSE 3.

The terms “subgenomic transcript” or “subgenomic RNA” synonymously referto a RNA molecule that is obtainable as a result of transcription usinga RNA molecule as template (“template RNA”), wherein the template RNAcomprises a subgenomic promoter that controls transcription of thesubgenomic transcript. The subgenomic transcript is obtainable in thepresence of an RNA-dependent RNA polymerase, in particular functionalalphavirus non-structural protein. For instance, the term “subgenomictranscript” may refer to the RNA transcript that is prepared in a cellinfected by an alphavirus, using the (−) strand complement of alphavirusgenomic RNA as template. However, the term “subgenomic transcript”, asused herein, is not limited thereto and also includes transcriptsobtainable by using heterologous RNA as template. For example,subgenomic transcripts are also obtainable by using the (−) strandcomplement of SGP-containing replicons according to the presentinvention as template. Thus, the term “subgenomic transcript” may referto a RNA molecule that is obtainable by transcribing a fragment ofalphavirus genomic RNA, as well as to a RNA molecule that is obtainableby transcribing a fragment of a replicon according to the presentinvention.

According to the invention, a nucleic acid construct that is capable ofbeing replicated by a replicase, preferably an alphaviral replicase, istermed replicon. According to the invention, the term “replicon” definesan RNA molecule that can be replicated by RNA-dependent RNA polymerase,yielding—without DNA intermediate—one or multiple identical oressentially identical copies of the RNA replicon. “Without DNAintermediate” means that no deoxyribonucleic acid (DNA) copy orcomplement of the replicon is formed in the process of forming thecopies of the RNA replicon, and/or that no deoxyribonucleic acid (DNA)molecule is used as a template in the process of forming the copies ofthe RNA replicon, or complement thereof. The replicase function istypically provided by functional alphavirus non-structural protein.

According to the invention, the terms “can be replicated” and “capableof being replicated” generally describe that one or more identical oressentially identical copies of a nucleic acid can be prepared. Whenused together with the term “replicase”, such as in “capable of beingreplicated by a replicase”, the terms “can be replicated” and “capableof being replicated” describe functional characteristics of a nucleicacid molecule, e.g. a RNA replicon, with respect to a replicase. Thesefunctional characteristics comprise at least one of (i) the replicase iscapable of recognizing the replicon and (ii) the replicase is capable ofacting as RNA-dependent RNA polymerase (RdRP). Preferably, the replicaseis capable of both (i) recognizing the replicon and (ii) acting asRNA-dependent RNA polymerase.

The expression “capable of recognizing” describes that the replicase iscapable of physically associating with the replicon, and preferably,that the replicase is capable of binding to the replicon, typicallynon-covalently. The term “binding” can mean that the replicase has thecapacity of binding to any one or more of a conserved sequence element 1(CSE 1) or complementary sequence thereof (if comprised by thereplicon), conserved sequence element 2 (CSE 2) or complementarysequence thereof (if comprised by the replicon), conserved sequenceelement 3 (CSE 3) or complementary sequence thereof (if comprised by thereplicon), conserved sequence element 4 (CSE 4) or complementarysequence thereof (if comprised by the replicon). Preferably, thereplicase is capable of binding to CSE 2 [i.e. to the (+) strand] and/orto CSE 4 [i.e. to the (+) strand], or of binding to the complement ofCSE 1 [i.e. to the (−) strand] and/or to the complement of CSE 3 [i.e.to the (−) strand].

The expression “capable of acting as RdRP” means that the replicase iscapable to catalyze the synthesis of the (−) strand complement ofalphaviral genomic (+) strand RNA, wherein the (+) strand RNA hastemplate function, and/or that the replicase is capable to catalyze thesynthesis of (+) strand alphaviral genomic RNA, wherein the (−) strandRNA has template function. In general, the expression “capable of actingas RdRP” can also include that the replicase is capable to catalyze thesynthesis of a (+) strand subgenomic transcript wherein a (−) strand RNAhas template function, and wherein synthesis of the (+) strandsubgenomic transcript is typically initiated at an alphavirus subgenomicpromoter.

The expressions “capable of binding” and “capable of acting as RdRP”refer to the capability at normal physiological conditions. Inparticular, they refer to the conditions inside a cell, which expressesfunctional alphavirus non-structural protein or which has beentransfected with a nucleic acid that codes for functional alphavirusnon-structural protein. The cell is preferably a eukaryotic cell. Thecapability of binding and/or the capability of acting as RdRP can beexperimentally tested, e.g. in a cell-free in vitro system or in aeukaryotic cell. Optionally, said eukaryotic cell is a cell from aspecies to which the particular alphavirus that represents the origin ofthe replicase is infectious. For example, when the alphavirus replicasefrom a particular alphavirus is used that is infectious to humans, thenormal physiological conditions are conditions in a human cell. Morepreferably, the eukaryotic cell (in one example human cell) is from thesame tissue or organ to which the particular alphavirus that representsthe origin of the replicase is infectious.

According to the invention, “compared to a native alphavirus sequence”and similar terms refer to a sequence that is a variant of a nativealphavirus sequence. The variant is typically not itself a nativealphavirus sequence.

In one embodiment, the RNA replicon comprises a replication recognitionsequence such as a 5′ replication recognition sequence and a 3′replication recognition sequence. A replication recognition sequence isa nucleic acid sequence that can be recognized by functional alphavirusnon-structural protein. In other words, functional alphavirusnon-structural protein is capable of recognizing the replicationrecognition sequence. Preferably, the 5′ replication recognitionsequence is located at the 5′ end of the replicon. In one embodiment,the 5′ replication recognition sequence consists of or comprises CSE 1and 2. Preferably, the 3′ replication recognition sequence is located atthe 3′ end of the replicon (if the replicon does not comprise a poly(A)tail), or immediately upstream of the poly(A) tail (if the repliconcomprises a poly(A) tail). In one embodiment, the 3′ replicationrecognition sequence consists of or comprises CSE 4.

In one embodiment, the 5′ replication recognition sequence and the 3′replication recognition sequence are capable of directing replication ofthe RNA replicon in the presence of functional alphavirus non-structuralprotein. Thus, when present alone or preferably together, theserecognition sequences direct replication of the RNA replicon in thepresence of functional alphavirus non-structural protein.

It is preferable that a functional alphavirus non-structural protein isprovided in cis (encoded as protein of interest by an open reading frameon the replicon) or in trans (encoded as protein of interest by an openreading frame on a separate replicase construct, that is capable ofrecognizing both the 5′ replication recognition sequence and the 3′replication recognition sequence of the replicon. In one embodiment,this is achieved when the 5′ and 3′ replication recognition sequencesare native to the alphavirus from which the functional alphavirusnon-structural protein is derived. Native means that the natural originof these sequences is the same alphavirus. In an alternative embodiment,the 5′ replication recognition sequence and/or the 3′ replicationrecognition sequence are not native to the alphavirus from which thefunctional alphavirus non-structural protein is derived, provided thatthe functional alphavirus non-structural protein is capable ofrecognizing both the 5′ replication recognition sequence and the 3′replication recognition sequence of the replicon. In other words, thefunctional alphavirus non-structural protein is compatible to the 5′replication recognition sequence and the 3′ replication recognitionsequence. When a non-native functional alphavirus non-structural proteinis capable of recognizing a respective sequence or sequence element, thefunctional alphavirus non-structural protein is said to be compatible(cross-virus compatibility). Any combination of (3′/5′) replicationrecognition sequences and CSEs, respectively, with functional alphavirusnon-structural protein is possible as long as cross-virus compatibilityexists. Cross-virus compatibility can readily be tested by the skilledperson working the present invention by incubating a functionalalphavirus non-structural protein to be tested together with an RNA,wherein the RNA has 3′- and 5′ replication recognition sequences to betested, at conditions suitable for RNA replication, e.g. in a suitablehost cell. If replication occurs, the (3′/5′) replication recognitionsequences and the functional alphavirus non-structural protein aredetermined to be compatible.

In one embodiment of the invention, the replicon is part of atrans-replication system and thus, the replicon is a trans-replicon. Inthis embodiment, it is preferred that the RNA replicon does not comprisean open reading frame encoding functional alphavirus non-structuralprotein. Thus, in this embodiment, the present invention provides asystem comprising two nucleic acid molecules: a first RNA construct forexpressing functional alphavirus non-structural protein (i.e. encodingfunctional alphavirus non-structural protein); and a second RNAmolecule, the RNA replicon. The RNA construct for expressing functionalalphavirus non-structural protein is synonymously referred to herein as“RNA construct for expressing functional alphavirus non-structuralprotein” or as “replicase construct”. The functional alphavirusnon-structural protein is as defined above and is typically encoded byan open reading frame comprised by the replicase construct. Thefunctional alphavirus non-structural protein encoded by the replicaseconstruct may be any functional alphavirus non-structural protein thatis capable of replicating the replicon. According to the invention, thereplicase construct may be present with the replicon(s) within the samecomposition, e.g. as mixed particulate formulation or combinedparticulate formulation, or in separate compositions, e.g. as individualparticulate formulations. When the system of the present invention isintroduced into a cell, preferably a eukaryotic cell, the open readingframe encoding functional alphavirus non-structural protein can betranslated. After translation, the functional alphavirus non-structuralprotein is capable of replicating a separate RNA molecule (RNA replicon)in trans.

Herein, trans (e.g. in the context of trans-acting, trans-regulatory),in general, means “acting from a different molecule” (i.e.,intermolecular). It is the opposite of cis (e.g. in the context ofcis-acting, cis-regulatory), which, in general, means “acting from thesame molecule” (i.e., intramolecular). In the context of RNA synthesis(including transcription and RNA replication), a trans-acting elementincludes a nucleic acid sequence that contains a gene encoding an enzymecapable of RNA synthesis (RNA polymerase). The RNA polymerase uses asecond nucleic acid molecule, i.e. a nucleic acid molecule other thanthe one by which it is encoded, as template for the synthesis of RNA.Both the RNA polymerase and the nucleic acid sequence that contains agene encoding the RNA polymerase are said to “act in trans” on thesecond nucleic acid molecule. In the context of the present invention,the RNA polymerase encoded by the trans-acting RNA may be functionalalphavirus non-structural protein. The functional alphavirusnon-structural protein is capable of using a second nucleic acidmolecule, which is an RNA replicon, as template for the synthesis orRNA, including replication of the RNA replicon. The RNA replicon thatcan be replicated by the replicase in trans according to the presentinvention is synonymously referred to herein as “trans-replicon”.

According to the present invention, the role of the functionalalphavirus non-structural protein is to amplify the replicon, and toprepare a subgenomic transcript, if a subgenomic promoter is present onthe replicon. If the replicon encodes a gene of interest for expression,the expression levels of the gene of interest and/or the duration ofexpression may be regulated in trans by modifying the levels of thefunctional alphavirus non-structural protein.

The trans-replication system of the present invention comprises at leasttwo nucleic acid molecules. In a preferred embodiment, the systemconsists of exactly two RNA molecules, the replicon and the replicaseconstruct. In alternative preferred embodiments, the system comprisesmore than one replicon, each preferably encoding at least one protein ofinterest, and also comprises the replicase construct. In theseembodiments, the functional alphavirus non-structural protein encoded bythe replicase construct can act on each replicon to drive replicationand optionally production of subgenomic transcripts, respectively. Forexample, each replicon may encode a pharmaceutically active peptide orprotein. This is advantageous e.g. if vaccination of a subject againstseveral different antigens is desired.

Preferably, the replicase construct lacks at least one conservedsequence element (CSE) that is required for (−) strand synthesis basedon a (+) strand template, and/or for (+) strand synthesis based on a (−)strand template. More preferably, the replicase construct does notcomprise any alphaviral conserved sequence elements (CSEs). Inparticular, among the four CSEs of alphavirus (Strauss & Strauss,Microbiol. Rev., 1994, vol. 58, pp. 491-562; José et al., FutureMicrobiol., 2009, vol. 4, pp. 837-856), any one or more of the followingCSEs are preferably not present on the replicase construct: CSE 1; CSE2; CSE 3; CSE 4. Particularly in the absence of any one or morealphaviral CSE, the replicase construct of the present inventionresembles typical eukaryotic mRNA much more than it resembles alphaviralgenomic RNA.

The replicase construct of the present invention is preferablydistinguished from alphaviral genomic RNA at least in that it is notcapable of self-replication and/or that it does not comprise an openreading frame under the control of a sub-genomic promoter. When unableto self-replicate, the replicase construct may also be termed “suicideconstruct”.

The replicase construct according to the present invention is preferablya single stranded RNA molecule. The replicase construct according to thepresent invention is typically a (+) stranded RNA molecule. In oneembodiment, the replicase construct of the present invention is anisolated nucleic acid molecule.

In one embodiment, the RNA such as the replicon according to the presentinvention comprises at least one open reading frame encoding a peptideof interest or a protein of interest. In various embodiments, thepeptide or protein of interest is encoded by a heterologous nucleic acidsequence. According to the present invention, the term “heterologous”refers to the fact that a nucleic acid sequence is not naturallyfunctionally or structurally linked to a nucleic sequence such as analphavirus nucleic acid sequence.

The RNA according to the present invention may encode a singlepolypeptide or multiple polypeptides. Multiple polypeptides can beencoded as a single polypeptide (fusion polypeptide) or as separatepolypeptides. In some embodiments, the RNA according to the presentinvention may comprise more than one open reading frame, each of whichin the case of a replicon may independently be selected to be under thecontrol of a subgenomic promoter or not. Alternatively, a poly-proteinor fusion polypeptide comprises individual polypeptides separated by anoptionally autocatalytic protease cleavage site (e.g. foot-and-mouthdisease virus 2A protein), or an intein.

Proteins of interest may e.g. be selected from the group consisting ofreporter proteins, pharmaceutically active peptides or proteins,inhibitors of intracellular interferon (IFN) signaling, and functionalalphavirus non-structural protein.

According to the invention, the term “peptide” comprises oligo- andpolypeptides and refers to substances which comprise two or more,preferably 3 or more, preferably 4 or more, preferably 6 or more,preferably 8 or more, preferably 10 or more, preferably 13 or more,preferably 16 or more, preferably 20 or more, and up to preferably 50,preferably 100 or preferably 150, consecutive amino acids linked to oneanother via peptide bonds. The term “protein” refers to large peptides,preferably peptides having at least 151 amino acids, but the terms“peptide” and “protein” are used herein usually as synonyms.

The terms “peptide” and “protein” comprise, according to the invention,substances which contain not only amino acid components but alsonon-amino acid components such as sugars and phosphate structures, andalso comprise substances containing bonds such as ester, thioether ordisulfide bonds.

The term “variant” with respect to, for example, nucleic acid and aminoacid sequences, according to the invention includes any variants, inparticular mutants, viral strain variants, splice variants,conformations, isoforms, allelic variants, species variants and specieshomologs, in particular those which are naturally present. An allelicvariant relates to an alteration in the normal sequence of a gene, thesignificance of which is often unclear. Complete gene sequencing oftenidentifies numerous allelic variants for a given gene. With respect tonucleic acid molecules, the term “variant” includes degenerate nucleicacid sequences, wherein a degenerate nucleic acid according to theinvention is a nucleic acid that differs from a reference nucleic acidin codon sequence due to the degeneracy of the genetic code (e.g. due toadaption of the codon usage). A species homolog is a nucleic acid oramino acid sequence with a different species of origin from that of agiven nucleic acid or amino acid sequence. A virus homolog is a nucleicacid or amino acid sequence with a different virus of origin from thatof a given nucleic acid or amino acid sequence.

According to the invention, nucleic acid variants include single ormultiple nucleotide deletions, additions, mutations, substitutionsand/or insertions in comparison with the reference nucleic acid.Deletions include removal of one or more nucleotides from the referencenucleic acid. Addition variants comprise 5′- and/or 3-terminal fusionsof one or more nucleotides, such as 1, 2, 3, 5, 10, 20, 30, 50, or morenucleotides. In the case of substitutions, at least one nucleotide inthe sequence is removed and at least one other nucleotide is inserted inits place (such as transversions and transitions). Mutations includeabasic sites, crosslinked sites, and chemically altered or modifiedbases. Insertions include the addition of at least one nucleotide intothe reference nucleic acid.

According to the invention, “nucleotide change” can refer to single ormultiple nucleotide deletions, additions, mutations, substitutionsand/or insertions in comparison with the reference nucleic acid. In someembodiments, a “nucleotide change” is selected from the group consistingof a deletion of a single nucleotide, the addition of a singlenucleotide, the mutation of a single nucleotide, the substitution of asingle nucleotide and/or the insertion of a single nucleotide, incomparison with the reference nucleic acid. According to the invention,a nucleic acid variant can comprise one or more nucleotide changes incomparison with the reference nucleic acid.

Variants of specific nucleic acid sequences preferably have at least onefunctional property of said specific sequences and preferably arefunctionally equivalent to said specific sequences, e.g. nucleic acidsequences exhibiting properties identical or similar to those of thespecific nucleic acid sequences.

Preferably the degree of identity between a given nucleic acid sequenceand a nucleic acid sequence which is a variant of said given nucleicacid sequence will be at least 70%, preferably at least 75%, preferablyat least 80%, more preferably at least 85%, even more preferably atleast 90% or most preferably at least 95%, 96%, 97%, 98% or 99%. Thedegree of identity is preferably given for a region of at least about30, at least about 50, at least about 70, at least about 90, at leastabout 100, at least about 150, at least about 200, at least about 250,at least about 300, or at least about 400 nucleotides. In preferredembodiments, the degree of identity is given for the entire length ofthe reference nucleic acid sequence.

“Sequence similarity” indicates the percentage of amino acids thateither are identical or that represent conservative amino acidsubstitutions. “Sequence identity” between two polypeptide or nucleicacid sequences indicates the percentage of amino acids or nucleotidesthat are identical between the sequences.

The term “% identical” is intended to refer, in particular, to apercentage of nucleotides which are identical in an optimal alignmentbetween two sequences to be compared, with said percentage being purelystatistical, and the differences between the two sequences may berandomly distributed over the entire length of the sequence and thesequence to be compared may comprise additions or deletions incomparison with the reference sequence, in order to obtain optimalalignment between two sequences. Comparisons of two sequences areusually carried out by comparing said sequences, after optimalalignment, with respect to a segment or “window of comparison”, in orderto identify local regions of corresponding sequences. The optimalalignment for a comparison may be carried out manually or with the aidof the local homology algorithm by Smith and Waterman, 1981, Ads App.Math. 2, 482, with the aid of the local homology algorithm by Needlemanand Wunsch, 1970, J. Mol. Biol. 48, 443, and with the aid of thesimilarity search algorithm by Pearson and Lipman, 1988, Proc. NatlAcad. Sci. USA 85, 2444 or with the aid of computer programs using saidalgorithms (GAP, BESTFIT, FASTA, BLAST P, BLAST N and TFASTA inWisconsin Genetics Software Package, Genetics Computer Group, 575Science Drive, Madison, Wis.).

Percentage identity is obtained by determining the number of identicalpositions in which the sequences to be compared correspond, dividingthis number by the number of positions compared and multiplying thisresult by 100.

For example, the BLAST program “BLAST 2 sequences” which is available onthe website http://www.ncbi.nlm.nih.gov/blast/bl2seq/wblast2.cgi may beused.

A nucleic acid is “capable of hybridizing” or “hybridizes” to anothernucleic acid if the two sequences are complementary with one another. Anucleic acid is “complementary” to another nucleic acid if the twosequences are capable of forming a stable duplex with one another.According to the invention, hybridization is preferably carried outunder conditions which allow specific hybridization betweenpolynucleotides (stringent conditions). Stringent conditions aredescribed, for example, in Molecular Cloning: A Laboratory Manual, J.Sambrook et al., Editors, 2^(nd) Edition, Cold Spring Harbor Laboratorypress, Cold Spring Harbor, N.Y., 1989 or Current Protocols in MolecularBiology, F. M. Ausubel et al., Editors, John Wiley & Sons, Inc., NewYork and refer, for example, to hybridization at 65° C. in hybridizationbuffer (3.5×SSC, 0.02% Ficoll, 0.02% polyvinylpyrrolidone, 0.02% bovineserum albumin, 2.5 mM NaH₂PO₄ (pH 7), 0.5% SDS, 2 mM EDTA). SSC is 0.15M sodium chloride/0.15 M sodium citrate, pH 7. After hybridization, themembrane to which the DNA has been transferred is washed, for example,in 2×SSC at room temperature and then in 0.1-0.5×SSC/0.1×SDS attemperatures of up to 68° C.

A percent complementarity indicates the percentage of contiguousresidues in a nucleic acid molecule that can form hydrogen bonds (e.g.,Watson-Crick base pairing) with a second nucleic acid sequence (e.g., 5,6, 7, 8, 9, 10 out of 10 being 50%, 60%, 70%, 80%, 90%, and 100%complementary). “Perfectly complementary” or “fully complementary” meansthat all the contiguous residues of a nucleic acid sequence willhydrogen bond with the same number of contiguous residues in a secondnucleic acid sequence. Preferably, the degree of complementarityaccording to the invention is at least 70%, preferably at least 75%,preferably at least 80%, more preferably at least 85%, even morepreferably at least 90% or most preferably at least 95%, 96%, 97%, 98%or 99%. Most preferably, the degree of complementarity according to theinvention is 100%.

The term “derivative” comprises any chemical derivatization of a nucleicacid on a nucleotide base, on the sugar or on the phosphate. The term“derivative” also comprises nucleic acids which contain nucleotides andnucleotide analogs not occurring naturally. Preferably, a derivatizationof a nucleic acid increases its stability.

According to the invention, a “nucleic acid sequence which is derivedfrom a nucleic acid sequence” refers to a nucleic acid may be a variantof the nucleic acid from which it is derived.

In one embodiment, an open reading frame encodes a reporter protein. Inthat embodiment, the open reading frame comprises a reporter gene.Certain genes may be chosen as reporters because the characteristicsthey confer on cells or organisms expressing them may be readilyidentified and measured, or because they are selectable markers.Reporter genes are often used as an indication of whether a certain genehas been taken up by or expressed in the cell or organism population.Preferably, the expression product of the reporter gene is visuallydetectable. Common visually detectable reporter proteins typicallypossess fluorescent or luminescent proteins. Examples of specificreporter genes include the gene that encodes jellyfish green fluorescentprotein (GFP), which causes cells that express it to glow green underblue light, the enzyme luciferase, which catalyzes a reaction withluciferin to produce light, and the red fluorescent protein (RFP).Variants of any of these specific reporter genes are possible, as longas the variants possess visually detectable properties. For example,eGFP is a point mutant variant of GFP.

According to the invention, in one embodiment, RNA comprises or consistsof pharmaceutically active RNA. A “pharmaceutically active RNA” may beRNA that encodes a pharmaceutically active peptide or protein.Preferably, the RNA according to the present invention encodes apharmaceutically active peptide or protein. Preferably, an open readingframe encodes a pharmaceutically active peptide or protein. Preferably,the RNA comprises an open reading frame that encodes a pharmaceuticallyactive peptide or protein, optionally in the case of an RNA repliconunder control of a subgenomic promoter.

A “pharmaceutically active peptide or protein” has a positive oradvantageous effect on the condition or disease state of a subject whenadministered to the subject in a therapeutically effective amount.Preferably, a pharmaceutically active peptide or protein has curative orpalliative properties and may be administered to ameliorate, relieve,alleviate, reverse, delay onset of or lessen the severity of one or moresymptoms of a disease or disorder. A pharmaceutically active peptide orprotein may have prophylactic properties and may be used to delay theonset of a disease or to lessen the severity of such disease orpathological condition. The term “pharmaceutically active peptide orprotein” includes entire proteins or polypeptides, and can also refer topharmaceutically active fragments thereof. It can also includepharmaceutically active analogs of a peptide or protein. The term“pharmaceutically active peptide or protein” includes peptides andproteins that are antigens, i.e., the peptide or protein elicits animmune response in a subject which may be therapeutic or partially orfully protective.

In one embodiment, the pharmaceutically active peptide or protein is orcomprises an immunologically active compound or an antigen or anepitope.

According to the invention, the term “immunologically active compound”relates to any compound altering an immune response, preferably byinducing and/or suppressing maturation of immune cells, inducing and/orsuppressing cytokine biosynthesis, and/or altering humoral immunity bystimulating antibody production by B cells. In one embodiment, theimmune response involves stimulation of an antibody response (usuallyincluding immunoglobulin G (IgG)) and/or a cellular response such as a Tcell response. Immunologically active compounds may possess potentimmunostimulating activity including, but not limited to, antiviral andantitumor activity, and can also down-regulate other aspects of theimmune response, for example shifting the immune response away from aTH₂ immune response, which is useful for treating a wide range of TH₂mediated diseases.

According to the invention, the term “antigen” or “immunogen” covers anysubstance that will elicit an immune response. In particular, an“antigen” relates to any substance that reacts specifically withantibodies or T-lymphocytes (T-cells). According to the presentinvention, the term “antigen” comprises any molecule which comprises atleast one epitope. Preferably, an antigen in the context of the presentinvention is a molecule which, optionally after processing, induces animmune reaction, which is preferably specific for the antigen. Accordingto the present invention, any suitable antigen may be used, which is acandidate for an immune reaction, wherein the immune reaction may beboth a humoral as well as a cellular immune reaction. In the context ofthe embodiments of the present invention, the antigen is preferablypresented by a cell, preferably by an antigen presenting cell, in thecontext of MHC molecules, which results in an immune reaction againstthe antigen. An antigen is preferably a product which corresponds to oris derived from a naturally occurring antigen. Such naturally occurringantigens may include or may be derived from allergens, viruses,bacteria, fungi, parasites and other infectious agents and pathogens oran antigen may also be a tumor antigen. According to the presentinvention, an antigen may correspond to a naturally occurring product,for example, a viral protein, or a part thereof. In preferredembodiments, the antigen is a surface polypeptide, i.e. a polypeptidenaturally displayed on the surface of a cell, a pathogen, a bacterium, avirus, a fungus, a parasite, an allergen, or a tumor. The antigen mayelicit an immune response against a cell, a pathogen, a bacterium, avirus, a fungus, a parasite, an allergen, or a tumor.

The term “disease-associated antigen” is used in it broadest sense torefer to any antigen associated with a disease. A disease-associatedantigen is a molecule which contains epitopes that will stimulate ahost's immune system to make a cellular antigen-specific immune responseand/or a humoral antibody response against the disease. Thedisease-associated antigen may therefore be used for therapeuticpurposes. Disease-associated antigens are preferably associated withinfection by microbes, typically microbial antigens, or associated withcancer, typically tumors.

The term “pathogen” refers to pathogenic biological material capable ofcausing disease in an organism, preferably a vertebrate organism.Pathogens include microorganisms such as bacteria, unicellulareukaryotic organisms (protozoa), fungi, as well as viruses.

The terms “epitope”, “antigen peptide”, “antigen epitope”, “immunogenicpeptide” and “MHC binding peptide” are used interchangeably herein andrefer to an antigenic determinant in a molecule such as an antigen,i.e., to a part in or fragment of an immunologically active compoundthat is recognized by the immune system, for example, that is recognizedby a T cell, in particular when presented in the context of MHCmolecules. An epitope of a protein preferably comprises a continuous ordiscontinuous portion of said protein and is preferably between 5 and100, preferably between 5 and 50, more preferably between 8 and 30, mostpreferably between 10 and 25 amino acids in length, for example, theepitope may be preferably 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,21, 22, 23, 24, or 25 amino acids in length. According to the inventionan epitope may bind to MHC molecules such as MHC molecules on thesurface of a cell and thus, may be a “MHC binding peptide” or “antigenpeptide”. The term “major histocompatibility complex” and theabbreviation “MHC” include MHC class I and MHC class II molecules andrelate to a complex of genes which is present in all vertebrates. MHCproteins or molecules are important for signaling between lymphocytesand antigen presenting cells or diseased cells in immune reactions,wherein the MHC proteins or molecules bind peptides and present them forrecognition by T cell receptors. The proteins encoded by the MHC areexpressed on the surface of cells, and display both self-antigens(peptide fragments from the cell itself) and non-self-antigens (e.g.,fragments of invading microorganisms) to a T cell. Preferred suchimmunogenic portions bind to an MHC class I or class molecule. As usedherein, an immunogenic portion is said to “bind to” an MHC class I orclass 11 molecule if such binding is detectable using any assay known inthe art. The term “MHC binding peptide” relates to a peptide which bindsto an MHC class I and/or an MHC class molecule. In the case of class IMHC/peptide complexes, the binding peptides are typically 8-10 aminoacids long although longer or shorter peptides may be effective. In thecase of class MHC/peptide complexes, the binding peptides are typically10-25 amino acids long and are in particular 13-18 amino acids long,whereas longer and shorter peptides may be effective.

In one embodiment, the protein of interest according to the presentinvention comprises an epitope suitable for vaccination of a targetorganism. A person skilled in the art will know that one of theprinciples of immunobiology and vaccination is based on the fact that animmunoprotective reaction to a disease is produced by immunizing anorganism with an antigen, which is immunologically relevant with respectto the disease to be treated. According to the present invention, anantigen is selected from the group comprising a self-antigen andnon-self-antigen. A non-self-antigen is preferably a bacterial antigen,a virus antigen, a fungus antigen, an allergen or a parasite antigen. Itis preferred that the antigen comprises an epitope that is capable ofeliciting an immune response in a target organism. For example, theepitope may elicit an immune response against a bacterium, a virus, afungus, a parasite, an allergen, or a tumor.

In some embodiments the non-self-antigen is a bacterial antigen. In someembodiments, the antigen elicits an immune response against a bacteriumwhich infects animals, including birds, fish and mammals, includingdomesticated animals. Preferably, the bacterium against which the immuneresponse is elicited is a pathogenic bacterium.

In some embodiments the non-self-antigen is a virus antigen. A virusantigen may for example be a protein, polypeptide or peptide from avirus surface protein, e.g. a membrane-bound glycoprotein, a capsidprotein or polypeptide or a spike protein or polypeptide. In someembodiments, the antigen elicits an immune response against a viruswhich infects animals, including birds, fish and mammals, includingdomesticated animals. Preferably, the virus against which the immuneresponse is elicited is a pathogenic virus.

In some embodiments the non-self-antigen is a polypeptide or a proteinfrom a fungus. In some embodiments, the antigen elicits an immuneresponse against a fungus which infects animals, including birds, fishand mammals, including domesticated animals. Preferably, the fungusagainst which the immune response is elicited is a pathogenic fungus.

In some embodiments the non-self-antigen is a polypeptide or proteinfrom a unicellular eukaryotic parasite. In some embodiments, the antigenelicits an immune response against a unicellular eukaryotic parasite,preferably a pathogenic unicellular eukaryotic parasite.

Pathogenic unicellular eukaryotic parasites may be e.g. from the genusPlasmodium, e.g. P. falciparum, P. vivax, P. malariae or P. ovale, fromthe genus Leishmania, or from the genus Trypanosoma, e.g. T. cruzi or T.brucei.

In some embodiments the non-self-antigen is an allergenic polypeptide oran allergenic protein. An allergenic protein or allergenic polypeptideis suitable for allergen immunotherapy, also known ashypo-sensitization.

In some embodiments the antigen is a self-antigen, particularly a tumorantigen. Tumor antigens and their determination are known to the skilledperson.

In the context of the present invention, the term “tumor antigen” or“tumor-associated antigen” relates to proteins that are under normalconditions specifically expressed in a limited number of tissues and/ororgans or in specific developmental stages, for example, the tumorantigen may be under normal conditions specifically expressed in stomachtissue, preferably in the gastric mucosa, in reproductive organs, e.g.,in testis, in trophoblastic tissue, e.g., in placenta, or in germ linecells, and are expressed or aberrantly expressed in one or more tumor orcancer tissues. In this context, “a limited number” preferably means notmore than 3, more preferably not more than 2. The tumor antigens in thecontext of the present invention include, for example, differentiationantigens, preferably cell type specific differentiation antigens, i.e.,proteins that are under normal conditions specifically expressed in acertain cell type at a certain differentiation stage, cancer/testisantigens, i.e., proteins that are under normal conditions specificallyexpressed in testis and sometimes in placenta, and germ line specificantigens. In the context of the present invention, the tumor antigen ispreferably associated with the cell surface of a cancer cell and ispreferably not or only rarely expressed in normal tissues. Preferably,the tumor antigen or the aberrant expression of the tumor antigenidentifies cancer cells. In the context of the present invention, thetumor antigen that is expressed by a cancer cell in a subject, e.g., apatient suffering from a cancer disease, is preferably a self-protein insaid subject. In preferred embodiments, the tumor antigen in the contextof the present invention is expressed under normal conditionsspecifically in a tissue or organ that is non-essential, i.e., tissuesor organs which when damaged by the immune system do not lead to deathof the subject, or in organs or structures of the body which are not oronly hardly accessible by the immune system. Preferably, the amino acidsequence of the tumor antigen is identical between the tumor antigenwhich is expressed in normal tissues and the tumor antigen which isexpressed in cancer tissues.

Examples for tumor antigens that may be useful in the present inventionare p53, ART-4, BAGE, beta-catenin/m, Bcr-abL CAMEL, CAP-1, CASP-8,CDC27/m, CDK4/m, CEA, the cell surface proteins of the claudin family,such as CLAUDIN-6, CLAUDIN-18.2 and CLAUDIN-12, c-MYC, CT, Cyp-B, DAM,ELF2M, ETV6-AML1, G250, GAGE, GnT-V, Gap100, HAGE, HER-2/neu, HPV-E7,HPV-E6, HAST-2, hTERT (or hTRT), LAGE, LDLR/FUT, MAGE-A, preferablyMAGE-A1, MAGE-A2, MAGE-A3, MAGE-A4, MAGE-A5, MAGE-A6, MAGE-A7, MAGE-A8,MAGE-A9, MAGE-A10, MAGE-A11, or MAGE-A12, MAGE-B, MAGE-C,MART-1/Melan-A, MC1R, Myosin/m, MUC1, MUM-1, -2, -3, NA88-A, NF1,NY-ESO-1, NY-BR-1, p190 minor BCR-abL, Pm1/RARa, PRAME, proteinase 3,PSA, PSM, RAGE, RU1 or RU2, SAGE, SART-1 or SART-3, SCGB3A2, SCP1, SCP2,SCP3, SSX, SURVIVIN, TEL/AML1, TPI/m, TRP-1, TRP-2, TRP-2/INT2, TPTE andWT. Particularly preferred tumor antigens include CLAUDIN-18.2(CLDN18.2) and CLAUDIN-6 (CLDN6). In some embodiments, it is notrequired that the pharmaceutically active peptide or protein is anantigen that elicits an immune response. Suitable pharmaceuticallyactive proteins or peptides may be selected from the group consisting ofcytokines and immune system proteins such as immunologically activecompounds (e.g., interleukins, colony stimulating factor (CSF),granulocyte colony stimulating factor (G-CSF), granulocyte-macrophagecolony stimulating factor (GM-CSF), erythropoietin, tumor necrosisfactor (TNF), interferons, integrins, addressins, seletins, homingreceptors, T cell receptors, immunoglobulins), hormones (insulin,thyroid hormone, catecholamines, gonadotrophines, trophic hormones,prolactin, oxytocin, dopamine, bovine somatotropin, leptins and thelike), growth hormones (e.g., human grown hormone), growth factors(e.g., epidermal growth factor, nerve growth factor, insulin-like growthfactor and the like), growth factor receptors, enzymes (tissueplasminogen activator, streptokinase, cholesterol biosynthetic ordegradative, steriodogenic enzymes, kinases, phosphodiesterases,methylases, de-methylases, dehydrogenases, cellulases, proteases,lipases, phospholipases, aromatases, cytochromes, adenylate orguanylaste cyclases, neuramidases and the like), receptors (steroidhormone receptors, peptide receptors), binding proteins (growth hormoneor growth factor binding proteins and the like), transcription andtranslation factors, tumor growth suppressing proteins (e.g., proteinswhich inhibit angiogenesis), structural proteins (such as collagen,fibroin, fibrinogen, elastin, tubulin, actin, and myosin), bloodproteins (thrombin, serum albumin, Factor VII, Factor VIII, insulin,Factor IX, Factor X, tissue plasminogen activator, protein C, vonWilebrand factor, antithrombin Ill, glucocerebrosidase, erythropoietingranulocyte colony stimulating factor (GCSF) or modified Factor VIII,anticoagulants and the like. In one embodiment, the pharmaceuticallyactive protein according to the invention is a cytokine which isinvolved in regulating lymphoid homeostasis, preferably a cytokine whichis involved in and preferably induces or enhances development, priming,expansion, differentiation and/or survival of T cells. In oneembodiment, the cytokine is an interleukin, e.g. IL-2, IL-7, IL-12,IL-15, or IL-21.

A further suitable protein of interest encoded by an open reading frameis an inhibitor of interferon (IFN) signaling. While it has beenreported that viability of cells in which RNA has been introduced forexpression can be reduced, in particular, if cells are transfectedmultiple times with RNA, IFN inhibiting agents were found to enhance theviability of cells in which RNA is to be expressed (WO 2014/071963 A1).Preferably, the inhibitor is an inhibitor of IFN type I signaling.Preventing engagement of IFN receptor by extracellular IFN andinhibiting intracellular IFN signaling in the cells allows stableexpression of RNA in the cells. Alternatively or additionally,preventing engagement of IFN receptor by extracellular IFN andinhibiting intracellular IFN signaling enhances survival of the cells,in particular, if cells are transfected repetitively with RNA. Withoutwishing to be bound by theory, it is envisaged that intracellular IFNsignalling can result in inhibition of translation and/or RNAdegradation. This can be addressed by inhibiting one or moreIFN-inducible antivirally active effector proteins. The IFN-inducibleantivirally active effector protein can be selected from the groupconsisting of RNA-dependent protein kinase (PKR), 2′,5′-oligoadenylatesynthetase (OAS) and RNaseL. Inhibiting intracellular IFN signalling maycomprise inhibiting the PKR-dependent pathway and/or the OAS-dependentpathway. A suitable protein of interest is a protein that is capable ofinhibiting the PKR-dependent pathway and/or the OAS-dependent pathway.Inhibiting the PKR-dependent pathway may comprise inhibiting eIF2-alphaphosphorylation. Inhibiting PKR may comprise treating the cell with atleast one PKR inhibitor. The PKR inhibitor may be a viral inhibitor ofPKR. The preferred viral inhibitor of PKR is vaccinia virus E3. If apeptide or protein (e.g. E3, K3) is to inhibit intracellular IFNsignaling, intracellular expression of the peptide or protein ispreferred. Vaccinia virus E3 is a 25 kDa dsRNA-binding protein (encodedby gene E3L) that binds and sequesters dsRNA to prevent the activationof PKR and OAS. E3 can bind directly to PKR and inhibits its activity,resulting in reduced phosphorylation of eIF2-alpha. Other suitableinhibitors of IFN signaling are Herpes simplex virus ICP34.5, Toscanavirus NSs, Bombyx mori nucleopolyhedrovirus PK2, and HCV NS34A.

In one embodiment, the inhibitor of intracellular or extracellular IFNsignaling is encoded by a replicon. The replicon comprises nucleic acidsequence elements that allow replication by alphavirus replicase,typically CSE 1, CSE 2 and CSE 4; and preferably also nucleic acidsequence elements that allow production of a subgenomic transcript, i.e.a subgenomic promoter, typically comprising CSE 3. The replicon mayadditionally comprise one or more non-polypeptide-sequence modifyingmodifications as described herein, e.g. cap, poly(A) sequence,adaptation of the codon usage. If multiple open reading frames arepresent on the replicon, then an inhibitor of intracellular IFNsignaling may be encoded by any one of them, optionally under control ofa subgenomic promoter or not. In a preferred embodiment, the inhibitorof intracellular IFN signaling is encoded by the most upstream openreading frame of the RNA replicon. When an inhibitor of intracellularIFN signaling is encoded by the most upstream open reading frame of theRNA replicon, the genetic information encoding the inhibitor ofintracellular IFN signaling will be translated early after introductionof the RNA replicon into a host cell, and the resulting protein maysubsequently inhibit intracellular IFN signaling.

A further suitable protein of interest encoded by an open reading frameis functional alphavirus non-structural protein. The term “alphavirusnon-structural protein” includes each and every co- orpost-translationally modified form, including carbohydrate-modified(such as glycosylated) and lipid-modified forms of alphavirusnon-structural protein.

In some embodiments, the term “alphavirus non-structural protein” refersto any one or more of individual non-structural proteins of alphavirusorigin (nsP1, nsP2, nsP3, nsP4), or to a poly-protein comprising thepolypeptide sequence of more than one non-structural protein ofalphavirus origin. In some embodiments, “alphavirus non-structuralprotein” refers to nsP123 and/or to nsP4. In other embodiments,“alphavirus non-structural protein” refers to nsP1234. In oneembodiment, the protein of interest encoded by an open reading frameconsists of all of nsP1, nsP2, nsP3 and nsP4 as one single, optionallycleavable poly-protein: nsP1234. In one embodiment, the protein ofinterest encoded by an open reading frame consists of nsP1, nsP2 andnsP3 as one single, optionally cleavable polyprotein: nsP123. In thatembodiment, nsP4 may be a further protein of interest and may be encodedby a further open reading frame.

In some embodiments, alphavirus non-structural protein is capable offorming a complex or association, e.g. in a host cell. In someembodiments, “alphavirus non-structural protein” refers to a complex orassociation of nsP123 (synonymously P123) and nsP4. In some embodiments,“alphavirus non-structural protein” refers to a complex or associationof nsP1, nsP2, and nsP3.

In some embodiments, “alphavirus non-structural protein” refers to acomplex or association of nsP1, nsP2, nsP3 and nsP4. In someembodiments, “alphavirus non-structural protein” refers to a complex orassociation of any one or more selected from the group consisting ofnsP1, nsP2, nsP3 and nsP4. In some embodiments, the alphavirusnon-structural protein comprises at least nsP4.

The terms “complex” or “association” refer to two or more same ordifferent protein molecules that are in spatial proximity. Proteins of acomplex are preferably in direct or indirect physical or physicochemicalcontact with each other. A complex or association can consist ofmultiple different proteins (heteromultimer) and/or of multiple copiesof one particular protein (homomultimer). In the context of alphavirusnon-structural protein, the term “complex or association” describes amultitude of at least two protein molecules, of which at least one is analphavirus non-structural protein. The complex or association canconsist of multiple copies of one particular protein (homomultimer)and/or of multiple different proteins (heteromultimer). In the contextof a multimer, “multi” means more than one, such as two, three, four,five, six, seven, eight, nine, ten, or more than ten.

The term “functional alphavirus non-structural protein” includesalphavirus non-structural protein that has replicase function. Thus,“functional alphavirus non-structural protein” includes alphavirusreplicase. “Replicase function” comprises the function of anRNA-dependent RNA polymerase (RdRP), i.e. an enzyme which is capable tocatalyze the synthesis of (−) strand RNA based on a (+) strand RNAtemplate, and/or which is capable to catalyze the synthesis of (+)strand RNA based on a (−) strand RNA template. Thus, the term“functional alphavirus non-structural protein” can refer to a protein orcomplex that synthesizes (−) stranded RNA, using the (+) stranded (e.g.genomic) RNA as template, to a protein or complex that synthesizes new(+) stranded RNA, using the (−) stranded complement of genomic RNA astemplate, and/or to a protein or complex that synthesizes a subgenomictranscript, using a fragment of the (−) stranded complement of genomicRNA as template. The functional alphavirus non-structural protein mayadditionally have one or more additional functions, such as e.g. aprotease (for auto-cleavage), helicase, terminal adenylyltransferase(for poly(A) tail addition), methyltransferase and guanylyltransferase(for providing a nucleic acid with a 5′-cap), nuclear localizationsites, triphosphatase (Gould et al., 2010, Antiviral Res., vol. 87 pp.111-124; Rupp et al., 2015, J. Gen. Virol., vol. 96, pp. 2483-500).

According to the invention, the term “alphavirus replicase” refers toalphaviral RNA-dependent RNA polymerase, including a RNA-dependent RNApolymerase from a naturally occurring alphavirus (alphavirus found innature) and a RNA-dependent RNA polymerase from a variant or derivativeof an alphavirus, such as from an attenuated alphavirus. In the contextof the present invention, the terms “replicase” and “alphavirusreplicase” are used interchangeably, unless the context dictates thatany particular replicase is not an alphavirus replicase.

The term “replicase” comprises all variants, in particularpost-translationally modified variants, conformations, isoforms andhomologs of alphavirus replicase, which are expressed byalphavirus-infected cells or which are expressed by cells that have beentransfected with a nucleic acid that codes for alphavirus replicase.Moreover, the term “replicase” comprises all forms of replicase thathave been produced and can be produced by recombinant methods. Forexample, a replicase comprising a tag that facilitates detection and/orpurification of the replicase in the laboratory, e.g. a myc-tag, aHA-tag or an oligohistidine tag (His-tag) may be produced by recombinantmethods.

Optionally, the alphavirus replicase is additionally functionallydefined by the capacity of binding to any one or more of alphavirusconserved sequence element 1 (CSE 1) or complementary sequence thereof,conserved sequence element 2 (CSE 2) or complementary sequence thereof,conserved sequence element 3 (CSE 3) or complementary sequence thereof,conserved sequence element 4 (CSE 4) or complementary sequence thereof.Preferably, the replicase is capable of binding to CSE 2 [i.e. to the(+) strand] and/or to CSE 4 [i.e. to the (+) strand], or of binding tothe complement of CSE 1 [i.e. to the (−) strand] and/or to thecomplement of CSE 3 [i.e. to the (−) strand].

The origin of the replicase is not limited to any particular alphavirus.In a preferred embodiment, the alphavirus replicase comprisesnon-structural protein from Semliki Forest virus, including a naturallyoccurring Semliki Forest virus and a variant or derivative of SemlikiForest virus, such as an attenuated Semliki Forest virus. In analternative preferred embodiment, the alphavirus replicase comprisesnon-structural protein from Sindbis virus, including a naturallyoccurring Sindbis virus and a variant or derivative of Sindbis virus,such as an attenuated Sindbis virus. In an alternative preferredembodiment, the alphavirus replicase comprises non-structural proteinfrom Venezuelan equine encephalitis virus (VEEV), including a naturallyoccurring VEEV and a variant or derivative of VEEV, such as anattenuated VEEV. In an alternative preferred embodiment, the alphavirusreplicase comprises non-structural protein from chikungunya virus(CHIKV), including a naturally occurring CHIKV and a variant orderivative of CHIKV, such as an attenuated CHIKV.

A replicase can also comprise non-structural proteins from more than onealphavirus. Thus, heterologous complexes or associations comprisingalphavirus non-structural protein and having replicase function areequally comprised by the present invention. Merely for illustrativepurposes, replicase may comprise one or more non-structural proteins(e.g. nsP1, nsP2) from a first alphavirus, and one or morenon-structural proteins (nsP3, nsP4) from a second alphavirus.Non-structural proteins from more than one different alphavirus may beencoded by separate open reading frames, or may be encoded by a singleopen reading frame as poly-protein, e.g. nsP1234.

In some embodiments, functional alphavirus non-structural protein iscapable of forming membranous replication complexes and/or vacuoles incells in which the functional alphavirus non-structural protein isexpressed.

If functional alphavirus non-structural protein, i.e. alphavirusnon-structural protein with replicase function, is encoded by a nucleicacid molecule according to the present invention, it is preferable thatthe subgenomic promoter of the replicon, if present, is compatible withsaid replicase. Compatible in this context means that the alphavirusreplicase is capable of recognizing the subgenomic promoter, if present.In one embodiment, this is achieved when the subgenomic promoter isnative to the alphavirus from which the replicase is derived, i.e. thenatural origin of these sequences is the same alphavirus. In analternative embodiment, the subgenomic promoter is not native to thealphavirus from which the alphavirus replicase is derived, provided thatthe alphavirus replicase is capable of recognizing the subgenomicpromoter. In other words, the replicase is compatible with thesubgenomic promoter (cross-virus compatibility). Examples of cross-viruscompatibility concerning subgenomic promoter and replicase originatingfrom different alphaviruses are known in the art. Any combination ofsubgenomic promoter and replicase is possible as long as cross-viruscompatibility exists. Cross-virus compatibility can readily be tested bythe skilled person working the present invention by incubating areplicase to be tested together with an RNA, wherein the RNA has asubgenomic promoter to be tested, at conditions suitable for RNAsynthesis from the a subgenomic promoter. If a subgenomic transcript isprepared, the subgenomic promoter and the replicase are determined to becompatible. Various examples of cross-virus compatibility are known(reviewed by Strauss & Strauss, Microbiol. Rev., 1994, vol. 58, pp.491-562).

In the present invention, an open reading frame encoding functionalalphavirus non-structural protein can be provided on the RNA replicon,or alternatively, can be provided as separate nucleic acid molecule,e.g. mRNA molecule. A separate mRNA molecule may optionally comprisee.g. cap, 5′-UTR, 3′-UTR, poly(A) sequence, and/or adaptation of thecodon usage. The separate mRNA molecule may be provided in trans, asdescribed herein.

When an open reading frame encoding functional alphavirus non-structuralprotein is provided on the RNA replicon, the replicon can preferably bereplicated by the functional alphavirus non-structural protein. Inparticular, the RNA replicon that encodes functional alphavirusnon-structural protein can be replicated by the functional alphavirusnon-structural protein encoded by the replicon. This embodiment isstrongly preferred when no nucleic acid molecule encoding functionalalphavirus non-structural protein is provided in trans. In thisembodiment, cis-replication of the replicon is aimed at. In a preferredembodiment, the RNA replicon comprises an open reading frame encodingfunctional alphavirus non-structural protein as well as at least onefurther open reading frame encoding a protein of interest, and can bereplicated by the functional alphavirus non-structural protein.

If multiple open reading frames are present on the replicon, then thefunctional alphavirus non-structural protein may be encoded by any oneof them, optionally under control of a subgenomic promoter or not,preferably not under control of a subgenomic promoter. In a preferredembodiment, the functional alphavirus non-structural protein is encodedby the most upstream open reading frame of the RNA replicon. When thefunctional alphavirus non-structural protein is encoded by the mostupstream open reading frame of the RNA replicon, the genetic informationencoding functional alphavirus non-structural protein will be translatedearly after introduction of the RNA replicon into a host cell, and theresulting protein can subsequently drive replication, and optionallyproduction of a subgenomic transcript, in the host cell.

Presence of an open reading frame encoding functional alphavirusnon-structural protein, either comprised by the replicon or comprised bya separate nucleic acid molecule that is provided in trans, allows thatthe replicon is replicated, and consequently, that a gene of interestencoded by the replicon, optionally under control of a subgenomicpromoter, is expressed at high levels.

The RNA replicon is suitable for expression of one or more genesencoding a peptide of interest or a protein of interest, optionallyunder control of a subgenomic promoter. Various embodiments arepossible. One or more open reading frames, each encoding a peptide ofinterest or a protein of interest, can be present on the RNA replicon.The most upstream open reading frame of the RNA replicon is referred toas “first open reading frame”. In some embodiments, the “first openreading frame” is the only open reading frame of the RNA replicon.Optionally, one or more further open reading frames can be presentdownstream of the first open reading frame. One or more further openreading frames downstream of the first open reading frame may bereferred to as “second open reading frame”, “third open reading frame”and so on, in the order (5′ to 3′) in which they are present downstreamof the first open reading frame. Preferably, each open reading framecomprises a start codon (base triplet), typically AUG (in the RNAmolecule), corresponding to ATG (in a respective DNA molecule).

If the replicon comprises a 3′ replication recognition sequence, it ispreferred that all open reading frames are localized upstream of the 3′replication recognition sequence.

When the RNA replicon comprising one or more open reading frames isintroduced into a host cell, the replicon may serve directly as templatefor translation of the first open reading frame. Preferably, thereplicon comprises a 5-cap. This is helpful for expression of the geneencoded by the first open reading frame directly from the replicon.

In some embodiments, at least one open reading frame of the replicon isunder the control of a subgenomic promoter, preferably an alphavirussubgenomic promoter. The alphavirus subgenomic promoter is veryefficient, and is therefore suitable for heterologous gene expression athigh levels. Preferably, the subgenomic promoter is a promoter for asubgenomic transcript in an alphavirus. This means that the subgenomicpromoter is one which is native to an alphavirus and which preferablycontrols transcription of the open reading frame encoding one or morestructural proteins in said alphavirus. Alternatively, the subgenomicpromoter is a variant of a subgenomic promoter of an alphavirus; anyvariant which functions as promoter for subgenomic RNA transcription ina host cell is suitable. If the replicon comprises a subgenomicpromoter, it is preferred that the replicon comprises a conservedsequence element 3 (CSE 3) or a variant thereof.

Preferably, the at least one open reading frame under control of asubgenomic promoter is localized downstream of the subgenomic promoter.Preferably, the subgenomic promoter controls production of subgenomicRNA comprising a transcript of the open reading frame.

In some embodiments the first open reading frame is under control of asubgenomic promoter. When the first open reading frame is under controlof a subgenomic promoter, its localization resembles the localization ofthe open reading frame encoding structural proteins in the genome of analphavirus. When the first open reading frame is under control of thesubgenomic promoter, it is preferred that the gene encoded by the firstopen reading frame can be expressed both from the replicon as well asfrom a subgenomic transcript thereof (the latter in the presence offunctional alphavirus non-structural protein). One or more further openreading frames, each under control of a subgenomic promoter, may bepresent downstream of the first open reading frame that is under controlof a subgenomic promoter. The genes encoded by the one or more furtheropen reading frames, e.g. by the second open reading frame, may betranslated from one or more subgenomic transcripts, each under controlof a subgenomic promoter. For example, the RNA replicon may comprise asubgenomic promoter controlling production of a transcript that encodesa second protein of interest.

In other embodiments the first open reading frame is not under controlof a subgenomic promoter. When the first open reading frame is not undercontrol of a subgenomic promoter, the gene encoded by the first openreading frame can be expressed from the replicon. One or more furtheropen reading frames, each under control of a subgenomic promoter, may bepresent downstream of the first open reading frame. The genes encoded bythe one or more further open reading frames may be expressed fromsubgenomic transcripts.

In a cell which comprises the replicon according to the presentinvention, the replicon may be amplified by functional alphavirusnon-structural protein. Additionally, if the replicon comprises one ormore open reading frames under control of a subgenomic promoter, one ormore subgenomic transcripts are expected to be prepared by functionalalphavirus non-structural protein. Functional alphavirus non-structuralprotein may be provided in trans, or may be encoded by an open readingframe of the replicon.

If a replicon comprises more than one open reading frame encoding aprotein of interest, it is preferable that each open reading frameencodes a different protein, e.g. a different pharmaceutically activepeptide or protein. For example, the protein encoded by the second openreading frame is different from the protein encoded by the first openreading frame.

In some embodiments, the protein of interest encoded by the first and/ora further open reading frame, preferably by the first open readingframe, is functional alphavirus non-structural protein or an inhibitorof IFN signaling, e.g. E3. In some embodiments, the protein of interestencoded by the first and/or a further open reading frame, e.g. by thesecond open reading frame, is a pharmaceutically active peptide orprotein, or a reporter protein.

In one embodiment, the protein of interest encoded by the first openreading frame is functional alphavirus non-structural protein. In thatembodiment the replicon preferably comprises a 5′-cap. Particularly whenthe protein of interest encoded by the first open reading frame isfunctional alphavirus non-structural protein, and preferably when thereplicon comprises a 5′-cap, the nucleic acid sequence encodingfunctional alphavirus non-structural protein can be efficientlytranslated from the replicon, and the resulting protein can subsequentlydrive replication of the replicon and drive synthesis of subgenomictranscript(s). This embodiment may be preferred when no additionalnucleic acid molecule encoding functional alphavirus non-structuralprotein is used or present together with the replicon. In thisembodiment, cis-replication of the replicon is aimed at.

The compositions described herein may be administered for treatingdiseases such as those described herein, e.g. a disease associated withan antigen encoded by the RNA which is administered.

The term “disease” refers to an abnormal condition that affects the bodyof an individual. A disease is often construed as a medical conditionassociated with specific symptoms and signs. A disease may be caused byfactors originally from an external source, such as infectious disease,or it may be caused by internal dysfunctions, such as autoimmunediseases. In humans, “disease” is often used more broadly to refer toany condition that causes pain, dysfunction, distress, social problems,or death to the individual afflicted, or similar problems for those incontact with the individual. In this broader sense, it sometimesincludes injuries, disabilities, disorders, syndromes, infections,isolated symptoms, deviant behaviors, and atypical variations ofstructure and function, while in other contexts and for other purposesthese may be considered distinguishable categories. Diseases usuallyaffect individuals not only physically, but also emotionally, ascontracting and living with many diseases can alter one's perspective onlife, and one's personality.

The term “disease associated with an antigen” or “disease involving anantigen” refers to any disease which implicates an antigen, e.g. adisease which is characterized by the presence of an antigen. Thedisease involving an antigen can be an infectious disease, an autoimmunedisease, or a cancer disease or simply cancer. As mentioned above, theantigen may be a disease-associated antigen, such as a tumor-associatedantigen, a viral antigen, or a bacterial antigen.

The term “infectious disease” refers to any disease which can betransmitted from individual to individual or from organism to organism,and is caused by a microbial agent (e.g. common cold). Infectiousdiseases are known in the art and include, for example, a viral disease,a bacterial disease, or a parasitic disease, which diseases are causedby a virus, a bacterium, and a parasite, respectively. In this regard,the infectious disease can be, for example, hepatitis, sexuallytransmitted diseases (e.g. chlamydia or gonorrhea), tuberculosis,HIV/acquired immune deficiency syndrome (AIDS), diphtheria, hepatitis B,hepatitis C, cholera, severe acute respiratory syndrome (SARS), the birdflu, influenza, animal diseases like foot-and-mouth disease, Peste depetits ruminants, Porcine reproductive and respiratory syndrome virus orparasite diseases such as Chagas, Malaria and others.

The term “autoimmune disease” refers to any disease in which the bodyproduces an immunogenic (i.e. immune system) response to someconstituent of its own tissue. In other words, the immune system losesits ability to recognize some tissue or system within the body as selfand targets and attacks it as if it were foreign. Autoimmune diseasescan be classified into those in which predominantly one organ isaffected (e.g. hemolytic anemia and anti-immune thyroiditis), and thosein which the autoimmune disease process is diffused through many tissues(e.g. systemic lupus erythematosus). For example, multiple sclerosis isthought to be caused by T cells attacking the sheaths that surround thenerve fibers of the brain and spinal cord. This results in loss ofcoordination, weakness, and blurred vision. Autoimmune diseases areknown in the art and include, for instance, Hashimoto's thyroiditis,Grave's disease, lupus, multiple sclerosis, rheumatic arthritis,hemolytic anemia, anti-immune thyroiditis, systemic lupus erythematosus,celiac disease, Crohn's disease, colitis, diabetes, scleroderma,psoriasis, and the like.

The terms “cancer disease” or “cancer” refer to or describe thephysiological condition in an individual that is typically characterizedby unregulated cell growth. Examples of cancers include, but are notlimited to, carcinoma, lymphoma, blastoma, sarcoma, and leukemia. Moreparticularly, examples of such cancers include bone cancer, blood cancerlung cancer, liver cancer, pancreatic cancer, skin cancer, cancer of thehead or neck, cutaneous or intraocular melanoma, uterine cancer, ovariancancer, rectal cancer, cancer of the anal region, stomach cancer, coloncancer, breast cancer, prostate cancer, uterine cancer, carcinoma of thesexual and reproductive organs, Hodgkin's Disease, cancer of theesophagus, cancer of the small intestine, cancer of the endocrinesystem, cancer of the thyroid gland, cancer of the parathyroid gland,cancer of the adrenal gland, sarcoma of soft tissue, cancer of thebladder, cancer of the kidney, renal cell carcinoma, carcinoma of therenal pelvis, neoplasms of the central nervous system (CNS),neuroectodermal cancer, spinal axis tumors, glioma, meningioma, andpituitary adenoma. The term “cancer” according to the invention alsocomprises cancer metastases.

The term “immune response” relates to a reaction of the immune systemsuch as to immunogenic organisms, such as bacteria or viruses, cells orsubstances. The term “immune response” includes the innate immuneresponse and the adaptive immune response. Preferably, the immuneresponse is related to an activation of immune cells, an induction ofcytokine biosynthesis and/or antibody production.

It is preferred that the immune response induced by the compositions ofthe present invention comprises the steps of activation of antigenpresenting cells, such as dendritic cells and/or macrophages,presentation of an antigen or fragment thereof by said antigenpresenting cells and activation of cytotoxic T cells due to thispresentation.

The term “immune cells” refers to cells of the immune system involved indefending the body of an individual. The term “immune cells” encompassesspecific types of immune cells and their precursors including leucocytescomprising macrophages, monocytes (precursors of macrophages),granulocytes such as neutrophils, eosinophils and basophils, dendriticcells, mast cells, and lymphocytes such as B cells, T cells and naturalkiller (NK) cells. Macrophages, monocytes (precursors of macrophages),neutrophils, dendritic cells, and mast cells are phagocytic cells.

The term “immunotherapy” relates to the treatment of a disease orcondition by inducing, enhancing, or suppressing an immune response.Immunotherapies designed to elicit or amplify an immune response areclassified as activation immunotherapies, while immunotherapies thatreduce or suppress an immune response are classified as suppressionimmunotherapies. The term “immunotherapy” includes antigen immunizationor antigen vaccination, or tumor immunization or tumor vaccination. Theterm “immunotherapy” also relates to the manipulation of immuneresponses such that inappropriate immune responses are modulated intomore appropriate ones in the context of autoimmune diseases such asrheumatic arthritis, allergies, diabetes or multiple sclerosis.

The terms “immunization” or “vaccination” describe the process ofadministering an antigen to an individual with the purpose of inducingan immune response, for example, for therapeutic or prophylacticreasons.

The term “therapeutic treatment” or simply “treatment” relates to anytreatment which improves the health status and/or prolongs (increases)the lifespan of an individual. Said treatment may eliminate the diseasein an individual, arrest or slow the development of a disease in anindividual, inhibit or slow the development of a disease in anindividual, decrease the frequency or severity of symptoms in anindividual, and/or decrease the recurrence in an individual whocurrently has or who previously has had a disease.

The term “prophylactic treatment” or “preventive treatment” relates toany treatment that is intended to prevent a disease from occurring in anindividual. The terms “prophylactic treatment” or “preventive treatment”are used herein interchangeably.

The terms “protect”, “prevent”, “prophylactic”, “preventive”, or“protective” relate to the prevention and/or treatment of the occurrenceand/or the propagation of a disease, e.g. tumor, in an individual. Forexample, a prophylactic administration of an immunotherapy, e.g. byadministering the composition of the present invention, can protect thereceiving individual from the development of a tumor. For example, atherapeutic administration of an immunotherapy, e.g. by administeringthe composition of the present invention, can stop the development of adisease, e.g. lead to the inhibition of the progress/growth of a tumor.This comprises the deceleration of the progress/growth of the tumor, inparticular a disruption of the progression of the tumor, whichpreferably leads to elimination of the tumor. A therapeuticadministration of an immunotherapy may protect the individual, forexample, from the dissemination or metastasis of existing tumors.

The term “individual” or “subject” relates to vertebrates, particularlymammals. For example, mammals in the context of the present inventionare humans, non-human primates, domesticated mammals such as dogs, cats,sheep, cattle, goats, pigs, horses etc., laboratory animals such asmice, rats, rabbits, guinea pigs, etc. as well as animals in captivitysuch as animals of zoos. The term “subject” also relates tonon-mammalian vertebrates such as birds (particularly domesticated birdssuch as chicken, ducks, geese, turkeys) and to fish (particularly farmedfish, e.g. salmon or catfish). The term “animal” as used herein alsoincludes humans.

The agents such as polyplex particles described herein may beadministered in the form of any suitable pharmaceutical composition. Theterm “pharmaceutical composition” relates to a formulation comprising atherapeutically effective agent or a salt thereof, preferably togetherwith pharmaceutical excipients such as buffers, preservatives andtonicity modifiers. Said pharmaceutical composition is useful fortreating, preventing, or reducing the severity of a disease or disorderby administration of said pharmaceutical composition to an individual. Apharmaceutical composition is also known in the art as a pharmaceuticalformulation. The pharmaceutical composition can be administered locallyor systemically. In the context of the present invention, thepharmaceutical composition comprises the particles described herein.

The term “systemic administration” refers to the administration of atherapeutically effective agent such that the agent becomes widelydistributed in the body of an individual in significant amounts anddevelops a biological effect. According to the present invention, it ispreferred that administration is by parenteral administration.

The term “parenteral administration” refers to administration of atherapeutically effective agent such that the agent does not pass theintestine. The term “parenteral administration” includes intravenousadministration, subcutaneous administration, intradermal administrationor intraarterial administration but is not limited thereto.

In one particularly preferred embodiment, the composition according tothe present invention is administered to muscle tissue, such as skeletalmuscle. Intramuscular administration such as by intramuscular injectionthus is the preferred route of administration.

Administration can be achieved in various ways. In one embodiment, thecomposition according to the present invention is administered byinjection. In a preferred embodiment, injection is via a needle.Needle-free injection may be used as an alternative.

The pharmaceutical compositions of the present invention may comprise atleast one adjuvant. The term “adjuvant” relates to compounds, which whenadministered in combination with an antigen or antigen peptide to anindividual, prolong or enhance or accelerate an immune response. It isassumed that adjuvants exert their biological activity by one or moremechanisms, including an increase of the surface of the antigen, aprolongation of the retention of the antigen in the body, a retardationof the antigen release, targeting of the antigen to macrophages,increase of the uptake of the antigen, enhancement of antigenprocessing, stimulation of cytokine release, stimulation and activationof immune cells such as B cells, macrophages, dendritic cells, T cellsand unspecific activation of immune cells. Adjuvants comprise aheterogeneous group of compounds such as oil emulsions (e.g., Freund'sadjuvants), mineral compounds (such as alum), bacterial products (suchas Bordetella pertussis toxin), or immune-stimulating complexes.Examples for adjuvants include saponins, incomplete Freund's adjuvants,complete Freund's adjuvants, tocopherol or alum, but are not limitedthereto.

The pharmaceutical composition according to the present invention isgenerally applied in a “pharmaceutically effective amount” and in “apharmaceutically acceptable preparation”.

The term “pharmaceutically effective amount” refers to the amount whichachieves a desired reaction or a desired effect alone or together withfurther doses. In the case of the treatment of a particular disease, thedesired reaction preferably relates to inhibition of the course of thedisease. This comprises slowing down the progress of the disease and, inparticular, interrupting or reversing the progress of the disease. Thedesired reaction in a treatment of a disease may also be delay of theonset or a prevention of the onset of said disease or said condition. Aneffective amount of the compositions described herein will depend on thecondition to be treated, the severeness of the disease, the individualparameters of the patient, including age, physiological condition, sizeand weight, the duration of treatment, the type of an accompanyingtherapy (if present), the specific route of administration and similarfactors. Accordingly, the doses administered of the compositionsdescribed herein may depend on various of such parameters. In the casethat a reaction in a patient is insufficient with an initial dose,higher doses (or effectively higher doses achieved by a different, morelocalized route of administration) may be used.

The term “pharmaceutically acceptable” refers to the non-toxicity of amaterial which does not interact with the action of the active componentof the pharmaceutical composition.

The pharmaceutical compositions of the present invention may containsalts, buffers, preserving agents, carriers and optionally othertherapeutic agents. Preferably, the pharmaceutical compositions of thepresent invention comprise one or more pharmaceutically acceptablecarriers, diluents and/or excipients.

The term “excipient” is intended to indicate all substances in apharmaceutical composition which are not active ingredients such asbinders, lubricants, thickeners, surface active agents, preservatives,emulsifiers, buffers, flavoring agents, or colorants.

The term “diluent” relates a diluting and/or thinning agent. Moreover,the term “diluent” includes any one or more of fluid, liquid or solidsuspension and/or mixing media.

The term “carrier” relates to one or more compatible solid or liquidfillers or diluents, which are suitable for an administration to ahuman. The term “carrier” relates to a natural or synthetic organic orinorganic component which is combined with an active component in orderto facilitate the application of the active component. Preferably,carrier components are sterile liquids such as water or oils, includingthose which are derived from mineral oil, animals, or plants, such aspeanut oil, soy bean oil, sesame oil, sunflower oil, etc. Salt solutionsand aqueous dextrose and glycerin solutions may also be used as aqueouscarrier compounds.

Pharmaceutically acceptable carriers or diluents for therapeutic use arewell known in the pharmaceutical art, and are described, for example, inRemington's Pharmaceutical Sciences, Mack Publishing Co. (A. R Gennaroedit. 1985). Examples of suitable carriers include, for example,magnesium carbonate, magnesium stearate, talc, sugar, lactose, pectin,dextrin, starch, gelatin, tragacanth, methylcellulose, sodiumcarboxymethylcellulose, a low melting wax, cocoa butter, and the like.Examples of suitable diluents include ethanol, glycerol and water.

Pharmaceutical carriers, excipients or diluents can be selected withregard to the intended route of administration and standardpharmaceutical practice. The pharmaceutical compositions of the presentinvention may comprise as, or in addition to, the carrier(s),excipient(s) or diluent(s) any suitable binder(s), lubricant(s),suspending agent(s), coating agent(s), and/or solubilising agent(s).Examples of suitable binders include starch, gelatin, natural sugarssuch as glucose, anhydrous lactose, free-flow lactose, beta-lactose,corn sweeteners, natural and synthetic gums, such as acacia, tragacanthor sodium alginate, carboxymethyl cellulose and polyethylene glycol.Examples of suitable lubricants include sodium oleate, sodium stearate,magnesium stearate, sodium benzoate, sodium acetate, sodium chloride andthe like. Preservatives, stabilizers, dyes and even flavoring agents maybe provided in the pharmaceutical composition. Examples of preservativesinclude sodium benzoate, sorbic acid and esters of p-hydroxybenzoicacid. Antioxidants and suspending agents may be also used.

In one embodiment, the composition is an aqueous composition. Theaqueous composition may optionally comprise solutes, e.g. salts. In oneembodiment, the composition is in the form of a freeze-driedcomposition. A freeze-dried composition is obtainable by freeze-drying arespective aqueous composition.

The agents and compositions provided herein may be used alone or incombination with other therapeutic regimens such as surgery,irradiation, chemotherapy and/or bone marrow transplantation(autologous, syngeneic, allogeneic or unrelated).

The present invention is described in detail and is illustrated by thefigures and examples, which are used only for illustration purposes andare not meant to be limiting. Owing to the description and the examples,further embodiments which are likewise included in the invention areaccessible to the skilled worker.

EXAMPLES Example 1: In-Vitro Toxicity of Polyplexes

Materials and Methods

In vivo-jetPEI™ Reagent, Cat. #201-50G, was purchased fromPolyplus-Transfection (Illkirch, France). In vivo-jetPEI™ is provided at150 mM (expressed as the concentration of nitrogen residues) in sterileapyrogenic water. JetPEI was diluted in HEPES 10 mM, pH 7.1, glucose 5%(HBGx1) buffer to the desired concentrations (expressed as theconcentration of nitrogen residues).

In-Vitro Cytotoxicity Assay

HEK-293 cells were seeded in a 96-well plate (flat bottom) atconcentration of 2×10⁴ cells per well. The cells were maintained at 37°C. and 7.5% C02. After 24 h, the supernatant was discarded and replacedwith 50 μL of DMEM Medium (+10% FCS). PEI was diluted (1:5) in RPMImedium with 10% FCS and pre-incubated for ˜15 min. Then 50 μl of the PEIsolution was added to the cells to a final medium volume of 100 μl.After additional 18 h, XTT-Assay (XTT Cell Viability Kit #9095, NewEngland Biolabs GmbH, Frankfurt, Germany) was performed according to themanual instructions. The cell death data as a function of PEIconcentration was fitted using the sigmoidal equation:

Cell death %=bottom+Top−Bottom/1+10^((log IC) ⁵⁰^(−log Concentration)×(Hill slope))

FIG. 1A shows the toxicity of free pure PEI on HEK-293 cells in-vitro.IC₅₀=77 μM of nitrogens (free). FIG. 1B shows the toxicity ofPEI/Replicon-RNA polyplexes on HEK-293 cells in-vitro. IC₅₀=542 μM ofnitrogens (polyplex formulation).

Results and Conclusions

Free PEI leads to cell death at nitrogen concentration above 18 μM (FIG.1A). The final concentration of free PEI in the cell medium should bebelow the aforementioned limit in order to avoid toxicity problems.

Polyplexes cause less cell death than free PEI but their toxicity alsoincrease when the PEI concentration increases (FIG. 1B). The cell deathafter addition of polyplexes could be calculated using the equation:

Cell death %=21.13+78.59/(1+10{circumflex over( )}((−0.27−log(Concentration))*3.13))

For polyplexes of N/P 11.6 (RNA concentration of 10 mg/l, PEI=348 μM),the cell death is 36.8%, while for polyplexes of N/P 15.8 the cell deathis 52.3%.

Example 2: Stability Studies of Polyplexes

Materials and Methods

In vivo-jetPEI™ Reagent from example 1 was used. RNA that encodes forluciferase, Construct D1-824 Replicon, ID R076 1, was provided by RNABiochemistry unit (BioNTech RNA Pharmaceuticals GmbH, Mainz, Germany).

Preparation of Polyplexes

Prior to preparation, in-vivo jetPEI™ and the sugar solution wereequilibrated at room temperature. The preparation of the invivo-jetPEI™/RNA complexes was performed in a laminar flow hood using asterile sugar solutions (Table 1). The final concentration of the sugarin the formulation was 5-10% w/v.

All formulations were prepared at RNA concentration of 250 mg/l and N/Pratio of 11.6.

The preparation steps were:

-   -   1. The RNA was diluted using a concentrated sugar buffer (HBGx2,        MBGx2 or HBTx2) to prepare a solution of ½ the final volume.        Gentle vortex was applied.    -   2. The in-vivo jetPEI™ reagent was diluted using the same sugar        buffer and sterile water to prepare a solution of ⅗ the final        volume. Gentle vortex was applied.    -   3. Half of the volume from the diluted in-vivo jetPEI™ was added        rapidly to the diluted RNA all at once, and gentle vortex was        applied.    -   4. The polyplexes were incubated for 15 to 20 minutes at room        temperature, and then transferred to the appropriate storage        condition.

TABLE 1 Mediums for preparation and storage of polyplexes # MediumAbbreviation 1 Glucose 5% with HEPES 10 mM pH 7.1 HBG × 1 2 Trehalose10% with HEPES 10 mM, pH 7.1 HBT × 1 3 Trehalose 10% with HEPES 2.8 mMand HBT × 1 + EDTA EDTA 80 μM, pH 7.1 4 Glucose 10% with HEPES 20 mM, pH7.1 HBG × 2 5 Trehalose 20% with HEPES 20 mM, pH 7.1 HBT × 2

Lyophilization of Polyplexes

The formulations were placed in a benchtop manifold freeze-drier Epsilon2-4 LSCplus (Martin Christ Gefriertrocknungsanlagen GmbH, Osterode,Germany).

The samples were frozen to −40° C. (˜2° C./min) at 1 ATM. It took 60-90min.

The pressure was reduced to 0.2 ATM for 10 min at −40° C.

The samples were dried for 4 h at 0.2 ATM and −40° C.

The samples were heated to −16° C. at 0.2 ATM for 2 h (ramp).

The samples were continued to dry for 4 h at −16° C. & 0.2 ATM.

The pressure was reduced to 0.01 ATM for 10 min at −16° C.

The samples were continued to dry for 4 h at −16° C. & 0.01 ATM.

The samples were heated to 20° C. at 0.01 ATM for 2 h (ramp).

The samples were continued to dry for 8 h at 20° C. & 0.01 ATM.

RNA Release from Polyplexes

Twelve test tubes with 90 μl sample were prepared according to Table 2.

TABLE 2 Sample preparation for RNA integrity and concentrationmeasurements # Description  1 Polyplexes in HBG stored at RT  2Polyplexes in HBG stored at 4° C.  3 Polyplexes in HBG stored at −20° C. 4 Polyplexes in HBT stored at RT  5 Polyplexes in HBT stored at 4° C. 6 Polyplexes in HBT stored at −20° C.  7 Lyophilized Polyplexes in HBTstored at 4° C.  8 Free RNA 250 mg/l in HBG × 1  9 Free RNA 125 mg/l inHBG × 1 10 Free RNA 63 mg/l in HBG × 1 11 Free RNA 31 mg/l in HBG × 1 12HBG × 1

Ten μl of Heparin 50 g/l in NaCl 500 mM were added to each tube. Themixture was incubated for 20 min at 30° C. in a vortex machine withshaking speed of 300 rpm.

RNA Integrity

Five μl of the released RNA were used for Bioanalyzer measurement. TheRNA was mixed with 5 μl of formamide. The RNA integrity quantificationwas performed with the Agilent 2100 Bioanalyzer instrument. Agilent RNA6000 Nano Kit was equilibrated at room temperature for 30 minutes. “NanoGel Matrix” 400 μl was centrifuged at 1500 g for 10 minutes. Sixty fiveμL of the supernatant were mixed with 1 μL of well vortexed “Nano DyeConcentrate” and centrifuged at 15000 g for 10 minutes to obtain the“Gel-Dye-Mix”. The prepared samples were denaturated by heating for 10minutes at 70° C., and the “Nano Ladder” was also heated for 2 minutesat the same temperature. The Chip was primed using the “PrimingStation”, by adding 9 μL of “Gel-Dye-Mix” in the marked G position andpressurizing the chip for 30 seconds. Then 9 μL “Gel-Dye-Mix” were addedinto both other G positions. Seven and a half μL of “Marker” were addedinto the ladder position and 5 μL into every sample position. Thedenatured “Nano Ladder” (1.5 μL) was added to the ladder position andafterwards 1 μL of sample were added into all 12 sample wells (add 1 μLof H₂O to not used wells). The Chip was placed on IKA Vortex machine andvortex for 1 minute at 2000 rpm was applied. This chip was measured inthe instrument, and Replicon RNA peak was detected at 47-57 seconds. TheRNA integrity was calculated in Expert 2100 software using Smearanalysis by selecting the Replicon RNA region.

The relative RNA integrity % was calculated using the followingequation:

${{Relative}{RNA}{integrity}\%} = {100 \times \frac{{RNA}{integrity}{after}2{weeks}{of}{storage}}{{RNA}{integrity}1h{after}{the}{polypex}{preparation}}}$

In-Vitro Transfection Assay

C2C12 cells were seeded in a 96-well plate (flat bottom) atconcentration of 2×10∝cells per well. The cells were maintained at 37°C. and 7.5% CO₂. After 24 h, the supernatant was discarded and replacedwith 50 μL of DMEM Medium (+10% FCS). Polyplexes were diluted (1:5) inDMEM medium with 10% FCS and pre-incubated for −15 min. Then 50 μl ofthe polyplex solution was added to the cells to a final medium volume of100 μl. After additional 48 h, Bright-Glo™ Luciferase assay Cat. #E2610,Promega GmbH, Mannheim, Germany) was performed according to manualinstructions.

Relative luminescence % was calculated using the following equation:

${{Relative}{luminesce}{}\%} = {100 \times \frac{{Absolute}{luminesence}{after}8{days}{of}{storage}}{{Absolute}{luminesence}{after}{}16{hours}{of}{storage}}}$

FIG. 2 shows the relative luminescence from C2C12 muscle cells afterincubation with PEI/Replicon-RNA polyplexes at N/P 11.6 from differentstorage conditions after 1 week storage.

FIG. 3 shows the relative RNA integrity of PEI/Replicon-RNA polyplexesat N/P 11.6 at different storage conditions after 2 weeks storage.

Results and Conclusions

Polyplexes have poor storage stability at liquid state (4 and 25° C.).The stability of polyplexes is significantly better at solid state(frozen or lyophilized) than at liquid state. The storage stability ofpolyplexes in HBT+EDTA buffer in solid state is significantly betterthan the storage stability in HBGx1 buffer.

For polyplexes in HBT+EDTA, solid state long storage stability ispossible, while for polyplexes in HBGx1, liquid state long storagestability is very unlikely.

Polyplex formulations with Replicon-RNA could be stabilized by additionof trehalose 5-20% (w/v), EDTA 80 μM-5 mM.

Example 3: Description of Mw Calculation of Linear PEIs

Linear PEI is synthetized from 2-ethyl-2-oxazoline in two steps: First,poly(2-ethyl-2-oxazoline) is obtained by a ring-opening isomerizationpolymerization of 2-ethyl-2-oxazoline in the presence of initiators(FIG. 4). Then, PEOX (N-propionyl-PEI) is acid-hydrolyzed to cleave offthe N-propionyl groups to yield PEI (FIG. 5).

Complete deacylation of PEOX(N-propionyl-PEI) with a molecular weight of50 kDa gives a linear PEI with a molecular weight of 22 kDa.Determination of the molecular weight of the intermediate product (PEOX)is performed by gel permeation chromatography with a Refractive IndexDetector or Multi-angle Light Scattering Detector. The full technicaldetails are described in: Adib, Abdennaji, Fabrice Stock, and PatrickErbacher. “Method for Manufacturing Linear Polyethylenimine (PEI) forTransfection Purpose and Linear PEI Obtained with Such Method.” U.S.patent application Ser. No. 12/671,312.

According to this invention, PEIs, which were synthetized from PEOX withthe MWs range of 40-60 kDa, are the potent transfection reagents forReplicon-RNA.

PEI for use according to the invention can be purchased fromPolyplus-Transfection SA (Illkirch-Graffenstaden, France): in-vivoJetPEI, Polysciences Europe GmbH (Eppelheim, Germany): PEI MAX 40000,and Euromedex (Souffelweyersheim, France): Exgen 500.

Example 4: Aggregation Kinetics of Polyplexes

Materials and Methods

The polyplexes were prepared in HBGx1 at RNA concentration of 200 mg/L,as previously described in Example 2. They were diluted in HBGx1 andphosphate buffered saline pH 7.4 (PBS) to RNA concentration of 10 mg/l.The PBS was used in order to increase the ionic strength of solution. A96 well plate was cleaned by filtrated air before adding the dilutedpolyplexes to the plate. The sizes were measured by DynaPro plate readerII instrument from WYATT technology GmbH (Dernbach, Germany). Cumulantfit was used for size calculation of monomodal samples, whileregularization fit for multimodal samples.

FIG. 6 shows the aggregation kinetics of IVT (A) and Replicon (B)polyplexes with JetPEI at increasing salt concentrations.

Results and Conclusions

High ionic strength leads to increase in the size of the polyplexes(FIG. 6). The ionic strength of the polyplex formulation has to be <20mM in order to prevent aggregation of the polyplexes.

Example 5: Sterilization of Polyplexes by Filtration

Materials and Methods

Polyplexes were prepared at RNA concentration of 100 mg/L and N/P ratiosof 11.5, 13.5 and 15.5, as previously described in the section“Stability studies of polyplexes”.

RNA Concentration and Integrity

The RNA was released from the polyplexes by incubation with Heparin.Ninety μl of free RNA (100 mg/l) or polyplexes were mixed with 10 μl ofHeparin 20 g/l in Hepes 10 mM, pH 7.4, EDTA 1 mM. The mixture wasincubated for 20 min at 30° C. in the vortex machine. Five μl of thismixture was mixed with 5 μl of formamide. Next, the RNA integrity wasmeasured by Bioanalyzer with pico-chips. The RNA integrity wascalculated, as described in example 2. The RNA concentration by wasmeasured by Ribogreen assay with “Quant-iT RiboGreen RNA Reagent andKit” (Cat. #R11490, Thermo Fischer Scientific), according to themanufacturer instructions for the high sensitivity method. Briefly, themixture of polyplexes with heparin were incubated with Ribogreenfluorophore in Tris 10 mM, pH 7.5, EDTA 1 mM buffer. The fluorescence ofRibogreen was measured at excitation wavelength of 485 nm and emission535 nm.

PEI Concentration

A solution of CuSO4 23 mg (anhydrous) in 100 ml of NaAcetate 0.1 M, pH5.4 (CSS reagent) was prepared. CSS reagent 600 μl was mixed with thepolyplexes and incubated for 5 min at ambient temperature. Theabsorption of each solution was measured at 285 nm on a UVspectrophotometer against the blank using a 1 cm cuvette. A calibrationcurve with known PEI concentrations (0-1.55 mM) was prepared, and usedto calculate the PEI concentration in the unknown samples. A backgroundabsorption of free RNA was subtracted from all samples.

Measurement of Electrophoretic Mobility (μ)

The polyplexes were diluted to RNA concentration of 20 mg/l in HBGx1 in3.1 ml. Next they were centrifuged at 600 g for 2 min. Three samples of1.05 ml were prepared for each formulation in plastic cuvettes. Theelectrophoretic mobility of the polyplexes was measured by laser doplerelectrophoresis with the ξ-Wallis instrument (Corduan technologies,France). Medium resolution measurement with 1 sequence of 10 runs wasused for each sample. Measurement with low signal to noise ratios, orwith extreme μ (>3 or <−3 μm*cm/V*S) were excluded from the finalanalysis. All formulations were measured in triplicates.

Filtration of Polyplexes

Three tubes with 2.68 ml of polyplexes at three different N/P ratioswere prepared. The polyplexes (1.34 ml) were filtrated through sterileMillex-GP Med Syringe Filter Units with pores of 220 nm (Cat.#SLMPL25SS, Merck Millipore). Physicochemical properties were measuredbefore and after the filtration.

FIG. 7 shows the physicochemical parameters of polyplexes before(Prepared) and after (Filtered) the filtration. A and B. RNA wasreleased from the polyplexes by Heparin. Then Replicon-RNA integrity (A)was measured by capillary electrophoresis with the bioanalyzerinstrument. Replicon-RNA concentration (B) was measured by Ribogreenfluoresence. C. PEI concentration was measured by CuSO₄ assay. D.Electrophoretic mobility (μ) was measured by laser-Dopplerelectrophoresis.

Results and Conclusions

Syringe Filter Units are suitable method for sterilization ofpolyplexes. The polyplexes have to be small <120 nm in order tosterilize them by filtration. At N/P ratio 11.6 the phyisicochemicalproperties of the polyplexes are not changed by the filtration.

When then N/P ratio is increased above 11.6, then there is loss of RNAduring the filtration.

Example 6: Effect of PEI Purity on Transfection of Replicon-RNA/PEIFormulations

Materials and Methods

The following high-purity PEIs were purchased from Polyplus-TransfectionSA (Illkirch-Graffenstaden, France): in-vivo JetPEI and fromPolysciences Europe GmbH (Eppelheim, Germany): PEI MAX 40000.

The following regular-purity PEI was purchased from Polysciences EuropeGmbH (Eppelheim, Germany): PEI 25000.

The polyplexes were prepared in HBGx1 at RNA concentration of 100 mg/L,as previously described in Example 2.

In-Vivo Transfection

Mice are anaesthetized with isoflurane and posterior side of hind-legswere shaved and disinfected with 70% EtOH-solution. Twenty μl of theinvestigated formulations were injected into the musculus tibialisposterior muscle with an Insulin-syringe pre-equipped with a cannula of30 G in size. The mouse was observed until regaining consciousness forsigns of pain, suffering and distress.

At day of measurement, mice were injected i.p. with Luciferin-solution.Subsequently, mice were anesthetized with Isoflurane and placed on aheat mat (37° C.) inside the IVIS® Spectrum (Perkin Elmer) imagingchamber with constant supply of Isoflurane/oxygen via individualanesthesia masks. Five minutes after injection of luciferin, detectionof bioluminescence light over one minute via camera was performed.Resulting images were analyzed using the software “LivingImage” (PerkinElmer).

FIG. 8 shows a comparison of the chemical structures of highly pure PEIand regular purity PEI. n=58 for PEI of 25 kDa. The average number ofthe —CH2CH2NH— monomers in PEI 25 kD is 581, which is also the length ofthe contiguous stretch of potentially protonatable nitrogens. Assuming auniform distribution of the N-propionyl moieties in the regular PE125,its contiguous stretch of protonatable nitrogens is only 64.

FIG. 9 shows the transfection of C2C12 muscle cells in-vitro byReplicon-RNA polyplexes that were prepared using PEIs of differentpurity level at different N/P ratios.

According to FIG. 10, Replicon-RNA Polyplexes at N/P ratios of 1 (−) and11.6 (+) were prepared with highly pure PEI (jetPEI) and regular purityPEI (25 kDa). Free RNA was used as a control. The formulations wereinjected i.m. to the posterior limbs of the mice (n=3). Luminescencesignals were recorded from the muscles of the mice.

Results and Conclusions

Polyplexes, which were prepared using highly pure PEI, transfect musclecells in-vitro better than regular purity PEI. Polyplexes have thehighest transfection efficacy in-vivo at N/P 11.6 after i.m. injection.

Cationic polyplexes with highly pure PEI at N/P 11.6 can transfect themuscle tissue in-vivo significantly better (4-5 folds difference) thanfree Replicon-RNA.

Anionic polyplexes with highly pure PEI at N/P 1, polyplexes withregular purity PEI at N/P 1, and cationic polyplexes with regular purePEI at N/P 11.6 transfect the muscle tissue worse than freeReplicon-RNA.

Example 7: High Transfection Efficacy of Replicon-RNA by Pure PEIs fromDifferent Providers and Lyophilized Polyplexes

Materials and Methods

The following high-purity PEIs were purchased from Polyplus-TransfectionSA (Illkirch-Graffenstaden, France): in-vivo JetPEI, and Euromedex(Souffelweyersheim, France): Exgen 500 and from Polysciences Europe GmbH(Eppelheim, Germany): PEI MAX 40000.

The polyplexes were prepared in HBGx1 at RNA conentration of 100 mg/L,as previously described in Example 2. All formulations were prepared inHBGx1 buffer except of the lyophilized formulation, which was preparedin HBTx1 buffer. The lyophilization of the polyplexes in HBTx1 bufferwas performed, as previously described in Example 2. The formulationswere injected i.m. to the posterior limbs of the mice (n=3), and theluminesence signals were recorded from the muscles of the mice, aspreviously described in Example 6.

For the experiment of FIG. 11, Replicon-RNA Polyplexes at N/P ratios of7.7 and 11.6 were prepared with highly pure PEIs: jetPEI (fromPolyplus), PEI-Max 40000 (from Polyscience), and Exgen 500 (fromEurodamex).

TABLE 3 Mann Whitney test, two tailed, for statistical significance(P-value) of the difference between the formulations in FIG. 11.Hypothesis Day P Value Fresh JetPEI is different than PEI MAX 40000 N/P11.6  4 0.474 Fresh JetPEI is different than Exgen N/P 7.7  4 0.065Fresh JetPEI is different than lyophilized JetPEI  4 0.387 Fresh JetPEIis different than PEI MAX 40000 N/P 11.6  7 0.180 Fresh JetPEI isdifferent than Exgen N/P 7.7  7 0.009* Fresh JetPEI is different thanlyophilized JetPEI  7 0.065 Fresh JetPEI is different than PEI MAX 40000N/P 11.6 10 0.132 Fresh JetPEI is different than Exgen N/P 7.7 10 0.788Fresh JetPEI is different than lyophilized JetPEI 10 0.093 Fresh JetPEIis different than PEI MAX 40000 N/P 11.6  4-10 0.7 Fresh JetPEI isdifferent than Exgen N/P 7.7  4-10 0.7 Fresh JetPEI is different thanlyophilized JetPEI  4-10 0.7

FIG. 12 shows lyophilized cakes of JetPEI/Replicon-RNA polyplexes at N/P11.6 prepared with different buffers.

Results and Conclusions

Polyplexes of Replicon-RNA transfect the muscle tissue efficiently afteri.m. injection (FIG. 11). The high purity PEIs: jetPEI (from Polyplus),PEI-Max 40000 (from Polyscience), and Exgen 500 (from Eurodamex) couldbe used for the preparation of the polyplexes. Exgen-500 polyplexestransfect better at N/P 7.7 than 11.6.

The lyophilizate of polyplexes in trehalose has a cake-like morphology,while in glucose the lyophilizate collapses, and it is hard to dissolveit in water (FIG. 12).

Trehalose is preferable to Glucose for lyophilization of polyplexes. Thelyophilized polyplexes perform in-vivo similarly to freshly preparedliquid-polyplexes.

Example 8: Transfection of IVT-RNA to Muscle Cells by Pure PEIPolyplexes

Materials and Methods

In vivo-jetPEI™ Reagent, Cat. #201-50G, was purchased fromPolyplus-Transfection (Illkirch, France). In vitro transcribed (IVT)mRNA that encodes for luciferase, Construct pST1-475, was provided byRNA Biochemistry unit (Biontech RNA Pharmaceuticals, Mainz, Germany).

Polyplexes of IVT-RNA and PEI were prepared as previously described inExample 2. Different N/P ratios were prepared by keeping the RNAconcentration constant and increasing the PEI concentration.

Transfection of muscle cells in-vitro was performed as previouslydescribed in Example 2.

In-vivo transfection studies were performed as previously described inExample 6.

According to FIG. 13, C2C12 muscle cells were transfected in-vitro byIVT-RNA that encodes for luciferase. The RNA was complexes with JetPEIat different N/P ratios in HBGx1 buffer.

Luminescence signal was measured 24 h after the transfection.

According to FIG. 14, IVT-RNA Polyplexes at N/P ratios of 5.8 and 11.6were prepared with pure PEI in HBGx1 buffer. Free IVT-RNA in HBGx1buffer was used as a control. The formulations were injected i.m. to theposterior limbs of the mice (n=3) at RNA doses of 2-8 μg per injection.Luminescence signals were recorded from the muscles of the mice 6 hafter the injection.

Results and Conclusions

Polyplexes of IVT-RNA and highly-pure PEI can transfect muscle cellsefficiently in-vitro. There is a positive correlation between thetransfection efficiency and N/P ratio (FIG. 13). Free IVT-RNA does nottransfect the cells in-vitro.

Polyplexes with highly pure PEI at N/P ratios 5.8 and 11.6 transfect themuscle tissue in-vivo significantly worse than free IVT-RNA (FIG. 14).

Example 9: Effect of Particle Size and Preparation Conditions onTransfection by Replicon-RNA Polyplexes

Materials and Methods

Polyplexes of Replicon-RNA and PEI were prepared as previously describedin Example 2. The polyplexes were prepared at 5 different RNA: 100, 250,500, 750, 1000 mg/l. The PEI concentration was increased appropriatelyin order to keep the N/P ratio at 11.6 for all formulations.

Size of the polyplexes was measured as previously described in Example4.

Transfection of muscle cells in-vitro was performed as previouslydescribed in Example 2.

In-vivo transfection studies were performed as previously described inExample 6.

According to FIG. 15, polyplexes of Replicon-RNA and jetPEI wereprepared at different RNA concentration at N/P ratio 11.6 in HBGx1buffer. For size measurements by DLS the polyplexes were diluted to RNAconcentration of 10 mg/l.

According to FIG. 16, C2C12 muscle cells were transfected in-vitro bythe polyplexes from FIG. 16. The Luminescence signal was measured 24 hafter the transfection.

According to FIG. 17, Rep-RNA Polyplexes at N/P ratio 11.6 were preparedwith pure PEI in HBGx1 buffer at different RNA concentration as in FIG.16. The formulations were injected i.m. to the posterior limbs of themice (n=3) at RNA doses of 2-8 μg per injection. Luminesence signalswere recorded from the muscles of the mice.

Results and Conclusions

-   -   Polyplexes are good transfection agents for Replicon-RNA. The        bioactivity of the polyplexes in terms of efficiency of        RNA-translation in muscle tissue is not influenced by RNA        concentration (0.1-1 g/l) at time of polyplex formation.    -   Size of polyplexes in the range of 60-200 nm does not have an        effect of the transfection efficacy of the polyplexes in-vitro        and in-vivo (i.m. injection).

Example 10: Different Polyplexes Perform Differently after s.c. or i.m.Injections into Mice

Materials and Methods

In vivo-jetPEI™ Reagent, Cat. #201-50G, was purchased fromPolyplus-Transfection SA (Illkirch, France). Linear PEI 22 kDa wasprovided by Prof. Cheradame (Polytheragene, EVRY cedex, France). RNAthat encodes for luciferase, Construct D1-824 Replicon, ID 1600801, wasprovided by RNA Biochemistry unit (Biontech RNA Pharmaceuticals, Mainz,Germany).

Polyplexes with JetPEI were prepared in HBGx1 at RNA concentration of500 mg/L, as previously described in Example 2.

Polyplexes with Polytheragene-PEI were prepared similarly to theprocedure with JetPEI but with two modifications:

-   -   1. HEPES 10 mM, pH 7.4 buffer was used instead of HBGx1 for the        preparation of the polyplexes.    -   2. N/P ratio of 15.8 was used instead of 11.6.

The preparation of the Polyplexes with Polytheragene-PEI was performedaccording to the following article: Démoulins, Thomas, et al.“Polyethylenimine-based polyplex delivery of self-replicating RNAvaccines.” Nanomedicine: Nanotechnology, Biology and Medicine (2015).

The polyplexes were diluted in HBGx1 or Opti-MEM (Cat. #31985062, ThermoFisher Scientific, Schwerte, Germany) buffers to final RNAconcentrations of 5 mg/l for in-vitro studies and 100 mg/l for in-vivostudies.

In-vitro studies were performed as previously described in Examples 1and 2.

In vivo studies were performed as previously described in Example 6.

Results and Conclusions

FIG. 18 shows in-vitro studies with PEI/Replicon-RNA polyplexes on humanDendritic cells (DCs) and mouse muscle cells (C2C12) A. Toxicity(expressed as % of viable cells after treatment with polyplexes) B.Transfection (expressed as luminescence emission after treatment withpolyplexes). The transfection results are shown only for C2C12 cells.

For the results of FIG. 19, Replicon-RNA Polyplexes at N/P ratios 11.6or 15.8 were prepared with PEI from Polyplus or Polytheragene in HBGx1or Hepes 10 mM buffers. Before injection to mice the polyplexes werediluted in HBGx1 or Opti-MEM buffers. The formulations were injectedi.m. to the posterior limbs of the mice (n=3) at RNA doses of 2 μg perinjection. Luminesence signals were recorded from the muscles of themice.

Results and Conclusions

TABLE 4 Comparison between sizes of the different polyplexes PEIDiameter # manufacturer N/P Preparation Buffer Dilution Buffer (nm) PDI1 Polyplus 11.6 HEPES 10 mM, pH 7.1 HBGx1 112 0.277 2 Polyplus 15.8HBGx1 HBGx1 107 0.239 3 Polytheragene 15.8 HEPES 10 mM, pH 7.4Opti-MEM >1000 multimodal 4 Polytheragene 15.8 HEPES 10 mM, pH 7.4 HBGx194 0.237

Opti-MEM has higher ionic strength than 20 mM. In Opti-MEM, thepolyplexes aggregate fast (Table 4), therefore this formulation is notsuitable for pharmaceutical development.

The polyplexes described herein (PEI from polyplus, N/P 11.6, HBGx1)have very different characteristics than previously described polyplexes(PEI from polytheagene, N/P 15.8, Opti-MEM). In Opti-MEM, the polyplexeshave a diameter >1000 nm and multimodal size distribution. Thepolyplexes described herein have a diameter of −100 nm and lowpolydispersity.

In-vitro, all polyplexes are more toxic to dendritic cells than musclecells. Probably, dendritic cells uptake the polyplexes after s.c.injection, while muscle cells are transfected by the polyplexes afteri.m. injection.

The transfection of muscle-cells in-vitro by the polyplex describedherein and previously described polyplexes is similar.

The transfection in-vivo by the polyplexes described herein andpreviously described polyplexes is different and it depends on the routeof application. The polyplexes described herein transfect well afteri.m. injection and worse after s.c. injection. The previously describedpolyplexes do not transfect at all after i.m. injection, while weaksignal was observed after s.c. injection.

Example 11: Administration of Replicon RNA by i.m. Versus i.d.Injections into Mice

Replicon-RNA, which encodes to luciferase enzyme, was dissolved in HBGx1buffer or complexed in polyplexes, as described in example 2. Theseformulations were injected i.m. into the musculus tibialis posteriormuscles of Balb/c mice at doses of 2 μg of RNA. The mice wereanasthsized by isofluorance 4, 7, and 10 days after the injections.Then, they were injected with luciferin substrate and the luminesenceemission from the muscles was recorded by a CCD camera.

Photons deriving from Luciferase protein were collected over one minuteand are shown as an overlay with the photograph of the imaged mice (FIG.20A). FIG. 20B shows a graphical display of measured photons/second(p/s) at injection site.

Seven days after intradermal (i.d.) application of 2 μg non-formulatedHBGx1) or formulated Replicon-RNA encoding Luciferase to two injectionsites at the dorsal skin of Balb/c mice, the animals were subjected tonon-invasive in vivo bioluminescence imaging. Photons deriving fromLuciferase protein were collected over one minute and are shown as anoverlay with the photograph of the imaged mice. Black arrows indicatethe site of injection (FIG. 21A). FIG. 21B shows a graphical display ofmeasured photons/second (p/s) at injection site.

Example 12: Beneficial Effect of RNA Formulation as a Vaccine

Mice were immunized twice at test day 0 and 21 with either a compositionof the single stranded Replicon-RNA encoding the haemagglutinin (HA) ofthe H1N1 Influenza virus strain A/PuertoRico/8/1934 (H1N1/PR8)formulated with PEI with a N/P ratio of 11.6 a or the non-formulatedsingle stranded RNA. All animals received a dose of 1.25 μg RNA. A thirdgroup received only saline as a buffer control group. As shown in FIG.22A, 19 days after the first immunization and shortly before the secondimmunization, all animals that received the formulated RNA developed animmune response against the HA analyzed by virus neutralization assay(VNT, detection limit 1280). In contrast, only 5 out of 8 animalsreceiving the non-formulated RNA seroconverted against HA. As shown inFIG. 22B, 35 days after the first immunization, all RNA-receivinganimals were positive for HA-specific antibodies and the antibody titersagainst the HA increased. Animal titers of the formulated RNA group butnot the non-formulated RNA group became significantly higher compared tothe saline control group. As shown in FIG. 22C, 54 days afterimmunization, mice that received 1.25 μg formulated RNA encoding theH1N1/PR8-HA developed a significantly higher antibody titer compared toanimals that received 1.25 μg of the non-formulated RNA encoding theH1N1/PR8-HA (Significance was calculated using one-way ANOVA; *p<0.001).

Mice were immunized once at test day 0 with either a composition of thesingle stranded Replicon-RNA encoding the haemagglutinin (HA) of theH1N1 Influenza virus strain A/PuertoRico/8/1934 (H1N1/PR8) formulatedwith PEI with a specific N/P ratio of 11.6 a or the non-formulatedsingle stranded RNA. All animals received 0.25 μg RNA. A third groupreceived only saline as a buffer control group. As shown in FIG. 23A, 54days after the immunization, all RNA-receiving animals were positive forHA-specific antibodies, titers of the formulated RNA group becamesignificantly higher compared to the saline control group and to animalsthat received 0.25 μg of the non-formulated RNA encoding the H1N1/PR8-HA(Significance was calculated using one-way ANOVA; ** p<0.001; * p<0.05).55 days after the immunization all mice were infected with a 10foldmedian lethal dose (MLD₅₀) of H1N1/PR8. Survival was observed. As shownin FIG. 23B, all control animals died within 8 days. 4 out of 5 animalsthat received the non-formulated RNA encoding the H1N1/PR8-HA survivedthe challenge infection. In contrast, all mice receiving the formulatedRNA encoding the H1N1/PR8-HA survived the challenge infectiondemonstrating the beneficial effect of RNA/polyalkyleneiminecomposition.

Example 13: Spray Drying of Replicon RNA Formulated with PEI

The formulation was prepared with a N:P ratio of 12 by following thepipet scheme given in Table 1 two times and subsequent combination ofthe obtained material. Thereby, 5.0 mL of replicon RNA polyplexes with aRNA concentration of 0.1 mg/mL RNA were obtained.

Polymer mix: RNA mix: HBT2X wfi jetPEI RNA stock HBT2X [μL] [μL] [μL][μL] [μL] 250 940 60 250 1000

3.5 mL of this formulation were spray dried and 533 mg of material werecollected (yield: 76.1%). The particle size of the freshly preparedreplicon RNA polyplexes was not determined, as the material wasdischarged at the Büchi demo lab. The particle size (z-average) afterreconstitution with water (mixture: 20 mg spray dried polyplexes and 200μl wfi; resulting in 10 mM trehalose and a RNA concentration of 0.1mg/mL) was 289 nm and the PDI was 0.238 (Nicomp, 15 minutes). FIG. 24Ashows an in-vitro investigation of the luciferase expression of saRNApolyplexes after and before spray drying. The luciferase activity of thesaRNA is not lost due to the spray drying process. Differences in theabsolute height of the signals are due to the variances of the assay.

In an additional experiment, uncomplexed mRNA in 10% (w:v) trehalose wasspray dried and the integrity of the mRNA after spray drying wasinvestigated by capillary electrophoresis measurements.

2.50 mL Messenger RNA (R36-05.2-DP; c(RNA)=0.5 mg/mL; 10 mM Hepes; 0.1mM EDTA; pH 7.0) were mixed with 2.50 mL 20% (w:v) Trehalose solution(volume ration of 1:1) resulting in the following composition:c(RNA)=0.25 mg/mL; 10% (w/v) Trehalose; 5 mM Hepes; 0.05 mM EDTA. Duringspray drying, the sample material was held on ice. In total, 2.5 mL ofthis solution was spray dried. During spray drying, the outlettemperature increased from 33 to 37° C. within ten minutes. In order tolower the temperature increase, the gas flow was increased from 98 to101 L/min. During spray drying, the temperature further increased to 41°C. within the next 60 minutes. After complete spraying, 165 mg driedmaterial were collected (yield: 66.0%). For analysis of RNA integrity,the material was dissolved in wfi (mixture: 20 mg spray dried RNA and200 μl wfi; resulting in a Trehalose content of 10% and a RNAconcentration of 0.25 mg/mL). The dissolved RNA was analyzed by usingthe Agilent 2100 Bioanalyzer. The results of these analysis are depictedas electropherogram of spray dried RNA in FIG. 24B.

It was demonstrated, that the integrity of the uncomplexed RNA wasmaintained, spray drying did not lead to measurable RNA degradation.

Spray drying experiments were performed as follows:

The Nano Spray Dryer B-90 from Büchi was used for spray drying of RNAcontaining formulations. For preparation of these formulations, thefollowing compounds were used:

-   -   Messenger RNA (R36-05.2-DP, c(RNA)=0.5 mg/mL; 10 mM Hepes; 0.1        mM EDTA;    -   pH 7.0)    -   Replicon RNA encoding for Luciferase (D2 RNA-A1310 29-01        pST1-SFV4-TRON-l2m2-A30L70, wfi, c(RNA)=1 mg/mL)    -   Water for injection (wfi)    -   NaCl (1.5 M in wfi)    -   Trehalose 20% (w:v) in wfi (Pfanstiehl. Lot No: 35261A)    -   2× Hepes buffered Trehalose 20% (w:v) in wfi (Pfanstiehl. Lot        No: 35261A, 20 mM Hepes)    -   JetPEI (Polyplus; Lot. Nr.: 13081A1S; 150 mM nitrogen)

For spray drying, the following process parameters were chosen:

-   -   Nozzle: 4 μm    -   Inlet temperature: 80° C.    -   Outlet temperature: 30° C.    -   Gas flow: 98 mL/min    -   Applied current: 15.000 V; 350 μA

Prior to all experiments, the device is cleaned with RNAse Zapp andwiped with ethanol, and the cap was cleaned in an ultrasonic bath.

Example 14: Microfluidics for Polyplex Manufacturing

The NanoAssembr™ (Precision Nanosystems, BC, Vancouver, Canada) with theMicrofluidic Chip provided by the manufacturer (1029-036) was used. Forthe RNA, an in house manufactured Replicon RNA (Batch No. R071_1_2) wasused. Polyethylenimine (Max PEI 40) was from Polysciences (Eppelheim,Germany). As Syringes BD Plastipak 1 ml; 1508006, BD Biosciences(Heidelberg, Germany) were used. The two components were mixed at a 1:1ratio, using a flow rate of 12 ml/minute. Samples were prepared at twodifferent concentrations, namely 50 mg/l and 250 mg/l.

For particle size measurements using dynamic light scattering, a 380 ZLSsubmicron particle/zeta potential analyzer from Nicomp (PSS Nicomp,Santa Barbara, Calif.) was used.

For each condition, 1.5 ml were manufactured. Samples were diluted withHBG buffer for size measurements.

Pipetting scheme was as follows:

Preparation parameters Final Final RNA Stock solutions RNA tube PEI tubevolume N/P Conc. JetPEI HBGx2 JetPEI HBGx2 Water (μl) ratio (mg/l) RNA(g/l) (mM) RNA (μl) (μl) (μl) (μl) (μl) 2000 12 50 2.6 106.9 38 962 33.638 927.9 2000 12 250 2.6 106.9 192 808 201.9 231 567.4

Microfluidic mixing experiments were performed using a device thatcomprises a Y-type microfluidic mixer where two components, which areprovided in standard syringes, are mixed. The two components were mixedat a 1:1 ratio, using a constant flow rate of 12 ml/minute. Samples wereprepared at two different concentrations, namely 50 mg/l and 250 mg/l,and particle sizes of the obtained polyplexes were measured.

Polyplexes were manufactured with microfluidic devices, demonstratingfeasibility of continuous flow manufacturing for upscaling and GMPmanufacturing. Particle formation was possible without problems, and noindication for aggregate formation or clogging was observed. Particlesize was measured by dynamic light scattering. For polyplexesmanufactured at 0.05 mg/l, the size was about 123 nm, and for particlesmanufactured at 0.25 mg/ml, the size was about 314 nm. Details of theobtained results are given in the table below.

Concentration Size Channel mg/ml (nm) PDI ND Width 0.05 122.8 0.31 16717 0.25 314.2 0.247 116 45

All samples measured at a RNA conc. of 0.02 mg/ml (diluted with HBGx1)The feasibility of polyplex manufacturing by microfluidics wasdemonstrated. Manufacturing was performed with a simple Y-type mixer,and no particular procedures, such as hydrodynamic focusing, werenecessary in order to enable smooth manufacturing. Under suitableconditions, particles with a size well below 200 nm can be manufactured,enabling terminal sterile filtration with established and GMP compliantsterile filters. As no indication for aggregation or clogging was noted,it is concluded that upscaling to larger manufacturing batches will bepossible without problems. Further options for upscaling compriseparallelization of several, identical devices. Summarizing, the resultscan be taken as an indication for the general feasibility of GMPcompliant microfluidic manufacturing of PEI/RNA polyplexes.

Example 15: Sterilization of Polyplexes by Filtration

Polyplexes were prepared at Replicon-RNA concentration of 100 mg/L andN/P ratios of 11.5, 13.5 and 15.5, as previously described in thesection “Stability studies of polyplexes”.

Three tubes with 2.68 ml of polyplexes at three different N/P ratioswere prepared. The polyplexes (1.34 ml) were filtrated through sterileMillex-GP Med Syringe Filter Units with pores of 220 nm (Cat.#SLMPL25SS, Merck Millipore).

The polyplexes were diluted to an RNA concentration 10 mg/L in HBGx1.Next, they were diluted to an RNA concentration of 5 mg/l in NaCl 0.9%30 min before the addition to cells. C2C12 cells were seeded in a96-well plate (flat bottom) at a concentration of 2×10⁴ cells per well.The cells were maintained at 37° C. and 7.5% CO₂. After 24 h, thesupernatant was discarded and replaced with 50 μL of DMEM Medium (+10%FCS). Polyplexes were diluted (1:5) in DMEM medium with 10% FCS andpre-incubated for −15 min. Then 50 μl of the polyplex solution was addedto the cells to a final medium volume of 100 μl. After additional 48 h,Bright-Glo™ Luciferase assay (Cat. #E2610, Promega GmbH, Mannheim,Germany) was performed according to the manual of instruction.

In parallel to transfection also the cell number was measured using Cellproliferation Kit II (XTT. Roche, #11465015001). In both assays eachpolyplex-sample was tested in biological triplicates. As negativecontrol, cells will be seeded without treatment (“untreated”). For theXTT-assay also medium without cells, equivalent to background (BG) werealso seeded in triplicates. Finally, luminescence (Bright-Glo™) as wellas absorbance (XTT) were measured with a “infinite 200pro” reader(Tecan). The normalized luminescence was calculated by dividing theluminescence signal by the absorbance (proportional to the cell number).

FIG. 25 shows the normalized luminescence from C2C12 muscle cells afterincubation with PEI/Replicon-RNA polyplexes at different N/P ratios,before (Prepared) and after (Sterilized) sterile filtration.

It can be concluded that Syringe Filter Units are suitable forsterilization of polyplexes. The transfection efficacy of the polyplexesdoes not change due to the sterilization process.

Example 16: Optimizing the Polyplex Transfection by Combinations ofShort and Long PEI

Luciferase encoding Replicon-RNA was complexed with a genuinecombination of Short PEI between 0.6 and 11 kDA (e.g. either linearShort PEI 2.5 kDA or branched Short PEI 1.8 kDA) and Long PEI between 20and 40 kDa (e.g. 22 kDa in vivo/Jet PEI) at different combinations for atotal NP of 10 or 12 in MBG buffer (final concentration 5% w/v Glucose,10 mM MES, pH 6.1). In vivo/Jet PEI NP12 alone was used as a benchmark.Complexation of Short and Long PEI polyplexes took place in two steps:In the first step, complexation of Replicon-RNA was adjusted for desiredNP with in vivo/Jet PEI. In the second step, excess of Short PEI wasadded to the formulation to reach the desired total NP ratio; i.e. thefirst number defines the Long PEI NP and the second number the Short PEI(e.g. NP4+8=NP4 Long PEI and NP8 Short PEI). Luciferase assay wereperformed as previously described in Example 15.

Results are shown in FIG. 26. FIG. 26 A) indicates transfection efficacyof Short linear PEI and Long in vivo Jet PEI polyplexes at 250 ng ofRNA/well. FIG. 27 B) indicates transfection efficacy of Short branchedPEI and Long in vivo Jet PEI polyplexes at 250 ng of RNA/well.

Conclusion: In comparison to the benchmark results with Long PEI (e.g.in vivo Jet PEI) only, the transfection efficacy can be significantlyimproved by using combinations of Long PEI and Short PEI.

Interestingly, with regard to combinations with linear Short PEI theluciferase expression signal peaked in the first 24 hours aftertransfection, whereas with regard to combinations with branched ShortPEI the luciferase expression signal peaked in the first 48 hours aftertransfection. Thus, in situations where expression in a particular timeframe is desired, careful selection of the right Short PEI/Long PEIcombination is reasonable.

Example 17: Optimizing the Polyplex Transfection by Reducing the Amountof Long PEI

Secreted nano-luciferase encoding Replicon-RNA was complexed with agenuine combination of Short PEI (e.g. branched 1.8 kDA) and Long PEI(e.g. in vivo/Jet PEI) at different combinations for a total NP of 12 inMBG buffer (final concentration 5% w/v Glucose, 10 mM MES, pH 6.1). Invivo/Jet PEI NP12 was used as a benchmark. Complexation of Short+LongPEI polyplexes took place in two stets: In the first step, complexationof replicon-RNA was adjusted for desired NP with in vivo/Jet PEI. In thesecond step, excess of short PEI was added to the formulation to reachthe desired total NP ratio; i.e. the first number defines the Long PEINP and the second number the Short PEI (e.g. NP4+8=NP4 Long PEI and NP8Short PEI). Secreted Luciferase was measured according to manufacturerprotocol (Nano-GLO, Promega, USA) at 125 ng or RNA/well. Cell viabilityassays were performed as previously described in Example 15.

Results are shown in FIG. 27. Compared to the benchmark and for the sametotal NP ratio, higher expression levels were achieved withcombinations, e.g. NP4+8 and NP1.15+11. Thus, Transfection efficacy canbe significantly increased by reducing the concentration of long PEI inthe formulation and increasing the concentration of less toxic Short PEI(e.g. branched 1.8 kDa).

Example 18: Effect of Salt Variations and/or pH on TransfectionEfficiency In Vivo

BALB/c mice were purchased from Janvier Laboratories and implemented inthe experiment at an age of eight weeks. Prior injection of indicatedtest items, mice were subjected to isoflurane anesthesia and fur removedfrom hind legs using an electric razor. Subsequently, Replicon-RNA(saRNA)-PEI-polyplexes (e.g. saRNA-in vivo Jet PEI Polyplexes NP12) at aRNA dose of 2 μg were intramuscularly applied in 20 μL total volume toeach musculus tibialis posterior of three mice per group. Theformulations varied with respect to pH and/or salt concentrations (e.g.NaCl). At indicated time points mice were intraperitoneally injectedwith D-Luciferin solution (100 mg/kg body weight) and bioluminescencecaptured non-invasively in isoflurane anesthesised mice for 1 min viaIVIS® Spectrum Device (Perkin Elmer). Graphs display photons per second[p/s] of bioluminescence signal determined via Living Image® software(Perkin Elmer) in a manually defined region of interest (ROIs) withregard to muscle of mice (injection sites) in these pictures with atotal of six values/group.

The effect of salt variations (e.g. NaCl) on the transfection efficiencyis shown in FIG. 28. Intramuscular injections of Replicon-RNA-PEIpolyplexes at different N/P ratios led to long enduring bioluminescencesignals in muscle region of mice after measurement at days 3, 6, 9 and13. The detected signal strength increased from day 3 to day 6 (peak)after application but was detectable even at day 13. The most intensesignal in muscle region of mice could be detected at day 6 after i.m.injection in mice receiving Replicon-RNA-PEI polyplexes (e.g. Long PEIN/P 12) and addition of low concentrations (5 to 10 mM) salt.

The effect of pH variations on the transfection efficiency is shown inFIG. 29. Good results were obtained with Replicon RNA (saRNA)-PEIpolyplex formulations having pH values between 6.5 and 7.1, preferablybetween 6.5 and 6.9. The most intense signal could be detected with aReplicon-RNA-Long PEI NP12 formulation adjusted to pH 6.5. Asbenchmarks, Replicon-RNA-Jet PEI Polyplexes NP12 with unadjusted pH (BM)or HBG (20 mM HEPES, pH 7.4, 5 wt. % glucose) were used.

Example 19: PH Dependent Effects on the Electrophoretic Mobility andTransfection Efficiency of PEI Polyplexes In Vitro

Luciferase encoding Replicon-RNA was complexed with Long PEI (e.g. invivo jet PEI) at a N/P ratio of 4 in HBG buffer (final concentration4.5% w/v Glucose, 10 mM HEPES, pH 7.1) at room temperature for 15minutes and aliquoted in 11 samples. The pH of the samples was adjustedby the addition of HCl or NaOH depending on the final bulk pH to betested. Measurement of electrophoretic mobility (p) was performed asdescribed in Example 5. In vitro transfection of C2C12 mouse musclecells, luciferase and cell viability assays were performed as previouslydescribed in Example 15.

The pH dependent effects on the electrophoretic mobility andtransfection efficiency of PEI polyplexes in vitro are shown in FIGS. 30and 31. FIG. 30 indicates the electrophoretic mobility of in vivojetPEI/Replicon-RNA polyplexes (N/P 4) adjusted to different pH values.FIG. 31 shows the normalized luminescence from C2C12 muscle cells afterincubation with different dosages of in vivo jetPEI/Replicon-RNApolyplexes at a N/P ratio of 4 and different pH values (pH 6.5-pH 8.5).

The electrophoretic mobility of the polyplexes negatively correlatedwith the pH. Neutral polyplexes are obtained at approx. pH 8.9.Increasing the positive charge density on PEI polyplexes by reducing thebulk pH of the polyplex, preferably to pH values between 6.5 and 7.1,resulted in a higher transfection efficiency of C2C12 cells withoutaffecting the cell viability. PEI polymers contain primary and secondaryamines, whose protonation state depends on the bulk pH. Therefore, theresults suggest an efficient way to control the charge of the polyplexesand their transfection efficiency by adjusting and optimizing the bulkpH.

Example 20: Influence of Positive Charge Excess in Long PEI Formulations

Secreted nano-luciferase encoding Replicon-RNA was complexed indifferent NP ratios between 2-12 in MBG buffer (final concentration 5%w/v Glucose, 10 mM MES, pH 6.1). Secreted Luciferase is measuredaccording to manufacturer protocol (Nano-GLO, Promega, USA) at 125 ng orRNA/well. Excess of positive charges is calculated based on the Long PEI(i.e. in vivo/Jet PEI)-Replicon RNA NP ratio and the exact NP ratio atwhich total complexation takes places for this replicon-RNA & in vivoJet PEI. Difference between used NP ratio and know NP ratio for totalcomplexation allows calculation of the excess of positive charges in theformulation.

As an example, results relating to transfection with in vivo Jet PEIpolyplexes at 250 ng of RNA are shown in FIG. 32. In general, increasingthe concentration of positive charges in the formulation isexponentially proportional to the luciferase expression level. Excess ofpositive charges up to 30 nM by increasing the amount of PEI has beenproven to be beneficial.

Example 21: Optimizing the One Component PEI Polyplex Transfection byUsing 2-Step Complexation

If only one PEI variant (such as e.g. Long PEI) is used, transfectionefficiency can be improved by using a 2-step complexation method.Secreted nano-luciferase encoding Replicon-RNA was complexed in twosteps for a total NP of 12 in MBG buffer (final concentration 5% w/vGlucose, 10 mM MES, pH 6.1). In vivo/Jet PEI NP12 1-Step complexationwas used as a benchmark. For example, complexation in 2 steps using invivo Jet PEI took place as follows: In the first step, complexation ofreplicon-RNA was adjusted for desired initial NP. In the second step,excess of in vivo/Jet PEI was added to the formulation to reach thedesired total NP ratio; i.e. the first number defines the initial PEI NPand the second number the excess of given in vivo Jet PEI on the secondstep (e.g. NP4+8: NP4 Jet PEI in first step and NP8 Jet PEI in secondstep). Secreted Luciferase was measured according to manufacturerprotocol (Nano-GLO, Promega, USA) at 125 ng or RNA/well. Cell viabilityassay were performed as previously described in Example 15.

Results of 2 step complexation are shown in FIG. 33. Compared to thevivo/Jet PEI NP12 1-Step complexation benchmark and for the same totalNP ratio, higher expression levels were achieved with two stepscomplexation.

Example 22: Effect of Polyplex Formulation Buffer on ImmunizationEfficiency

saRNA was formulated into polyplexes by using In vivo-jetPEI. Polyplexeswere produced by using Hepes-buffered glucose (HBG) or MES-bufferedglucose (MBG) (5% D-Glucose, 10 mM MES, pH 6.1). Mice were immunizedi.m. at d0 in a one shot experiment. Serum was collected at d45 afterimmunization and the amount of Cf07-HA specific antibodies in the serumwas analyzed using HA-specific ELISA. Endpoint titration ofserumdilutions has been performed and the area under the curve (AUC) wasdetermined. Percentage increase in area under the curve of MBG-producedpolyplexes is depicted compared to HBG-produced polyplexes set as 100%.

Results are shown in FIG. 34. In comparison to polyplexes formulatedwith HBG, polyplexes produced by using MES-buffered glucose generate amuch higher ELISA signal after one shot vaccination of mice.

List of Abbreviations and Definitions

-   ATM atmospheric pressure-   C Concentration-   CSS a solution of CuSO₄ 23 mg in 100 ml of NaAcetate 0.1 M, pH 5.4-   DLS Dynamic light scattering-   EDTA Ethylenediaminetetraacetic acid-   FCS Fetal calf serum-   h hours-   HBG×1 HEPES 10 mM buffered (pH 7.1) glucose 5%-   HBG×2 HEPES 20 mM buffered (pH 7.1) glucose 10%-   HBT×1 HEPES 10 mM buffered (pH 7.1) trehalose 10%-   HBT×2 HEPES 20 mM buffered (pH 7.1) trehalose 20%-   HBT×1+EDTA HEPES 2.8 mM buffered (pH 7.1) trehalose 10% with EDTA 80    μM-   HEPES 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid-   IVI Institute of Virology and immunology, MittelhAusern, Switzerland-   IVT in-vitro transcribed mRNA-   kDa 1000 Daltons-   Lyo Lyophilization-   min minutes-   MBGx1 5% D-Glucose, 10 mM MES, pH 6.1-   MES 2-(N-morpholino)ethanesulfonic acid-   N/P the ratio between the number of amine groups in PEI and    phosphate groups in RNA.-   PEI Polyethyleneimine-   RNA Ribonucleic acid-   UV Ultraviolet

1.-51. (canceled)
 52. A composition comprising: (a) single stranded RNA;and (b) polyethyleneimine wherein the single stranded RNA and thepolyethyleneimine are present in polyplex particles and the molar ratioof the number of nitrogen atoms (N) in the polyethyleneimine to thenumber of phosphor atoms (P) in the single stranded RNA (N:P ratio) is2.0 to 15.0, wherein the ionic strength of the composition is 50 mM orless.
 53. The composition according to claim 52, wherein the N:P ratiois 6.0 to 12.0.
 54. The composition according to claim 52, wherein theconcentration of monovalent cationic ions is 25 mM or less and theconcentration of divalent cationic ions is 20 μM or less.
 55. Thecomposition according to claim 52, wherein the pH of the composition isbetween 4 and 8; between 5.5 and 8, between 6 and 7.5, between 6.5 and7.1, between 6.5 and 7, or between 6.5 and 6.9; or between 5 and 7.5.56. The composition according to claim 52, wherein the polyethyleneiminecomprises the following general formula (I):

wherein R is H; n is 2; and p is an integer, wherein p is such that theaverage molecular weight of the polymer is 1.5·10² to 10⁷ Da, 5000 to105 Da, 10000 to 40000 Da, 15000 to 30000 Da, or 20000 to 25000 Da. 57.The composition according to claim 52, wherein at least 92% of the Natoms in the polyethyleneimine are protonatable.
 58. The compositionaccording to claim 52, further comprising one or more additives.
 59. Thecomposition according to claim 58, wherein the one or more additives areselected from the group consisting of buffering substances, saccharides,stabilizers, cryoprotectants, lyoprotectants, and chelating agents. 60.The composition according to claim 59, wherein (i) the bufferingsubstances comprise at least one selected from the group consisting of4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES),3-morpholino-2-hydroxypropanesulfonic acid (MOPSO), acetic acid, acetatebuffers and analogues, phosphoric acid and phosphate buffers, and citricacid and citrate buffers; and/or (ii) the saccharides comprise at leastone selected from the group consisting of monosaccharides,disaccharides, trisaccharides, oligosaccharides, polysaccharides,glucose, trehalose, and saccharose; and/or (iii) the cryoprotectantscomprise at least one selected from the group consisting of glycols,ethylene glycol, propylene glycol, and glycerol; and/or (iv) thechelating agent comprises EDTA.
 61. The composition according to claim52, wherein the composition comprises HEPES buffered glucose (HBG),HEPES buffered trehalose (HBT), or MES-buffered glucose (MBG).
 62. Thecomposition according to claim 61, wherein the HBG comprises 5% glucose(w/v) and 10 mM HEPES, pH 7.1, the HBT comprises 10% trehalose (w/v) and10 mM HEPES, pH 7.1, or the MBG comprises 5% glucose (w/v) and 10 mMMES, pH 6.1.
 63. The composition according to claim 52, wherein: (i) thez-average as derived from dynamic light scattering measurements of theparticles is less than 200 nm, less than 150 nm, or less than 100 nm; orthe z-average size of the particles is between 50 nm and 200 nm; and/or(ii) the polydispersity index as derived from dynamic light scatteringmeasurements of the particles is less than 0.5, less than 0.3, or lessthan 0.2; and/or (iii) the Zeta-potential of the particles is 20 mV ormore, 20 to 40 mV, 20 to 25 mV or 25 to 40 mV; and/or (iv) the particlesare neutral or positively charged at physiological pH or at a pH between4.5 and 7.5.
 64. The composition according to claim 52, wherein thesingle stranded RNA is a molecule of 6000 to 15000 bases or of 9000 to12000 bases, and/or wherein the single stranded RNA: (i) encodes atleast one protein of interest; and/or (ii) is a replicon, aself-replicating, or a self-amplifying RNA; and/or (iii) comprises anopen reading frame encoding at least one peptide or protein of interest.65. The composition according to claim 64, wherein the replicon, theself-replicating or the self-amplifying RNA is derived from or compriseselements derived from an alphavirus and/or wherein the replicon can bereplicated by a replicase from an alphavirus and/or wherein the repliconcomprises a 5′ replication recognition sequence from an alphavirus and a3′ replication recognition sequence from an alphavirus.
 66. Thecomposition according to claim 65, wherein the alphavirus is Venezuelanequine encephalitis virus (VEEV).
 67. The composition according to claim64, wherein the peptide or protein of interest is a pharmaceuticallyactive peptide or protein
 68. The composition according to claim 52,wherein the composition is an aqueous composition.
 69. The compositionaccording to claim 52, wherein (i) the composition is a pharmaceuticalcomposition; and/or (ii) the composition is for use in therapy; and/or(iii) the composition is a vaccine composition; and/or (iv) thecomposition is for introducing RNA into a cell; and/or (v) thecomposition is for expressing RNA in a cell; and/or (vi) the compositionis for intramuscular administration of the RNA.
 70. A method forintroducing RNA into a cell of a patient in need thereof, said methodcomprising administering the composition according to claim 52 to thepatient.
 71. The method according to claim 70, wherein the cell is amuscle cell.
 72. A method of intramuscular administration of RNAcomprising the step of intramuscularly administering the compositionaccording to claim
 52. 73. A method for treating a cancer associatedwith a cancer-antigen in a subject, comprising administering thecomposition according to claim 52, wherein the single stranded RNAencodes the cancer-antigen.
 74. The composition according to claim 52,wherein the composition is a frozen, lyophilized or spray driedcomposition, wherein the composition comprises a cryoprotectant and/orlyoprotectant.
 75. The composition according to claim 74, wherein: (i)the lyoprotectant is a disaccharide or a polysaccharide; and/or (ii) thecomposition further comprises a chelating agent; and/or (iii) thecomposition comprises trehalose, saccharose, lactose, or maltose; and/or(iv) the composition is prepared from an aqueous composition comprisinga disaccharide at 5-20% (w/v).
 76. The composition according to claim75, wherein: (i) the disaccharide is trehalose or the polysaccharide isdextran; and/or (ii) the chelating agent is EDTA; and/or (iii) thechelating agent is at 80 μM to 10 mM; and/or (iv) the aqueouscomposition comprises trehalose, HEPES, and EDTA.
 77. The compositionaccording to claim 76, wherein the aqueous composition comprises 10%trehalose (w/v), 2.8 mM HEPES, 80 μM EDTA, pH 7.1.
 78. An aqueouscomposition obtainable by thawing the frozen composition, orreconstituting the lyophilized or spray dried composition according toclaim
 74. 79. A method of preparing a frozen, lyophilized or spray driedcomposition comprising: (i) preparing an aqueous composition accordingto claim 68 comprising a cryoprotectant and/or lyoprotectant and (ii)freezing, lyophilizing or spray drying the composition.
 80. The methodaccording to claim 79, wherein: (i) the lyoprotectant is a disaccharideor a polysaccharide; and/or (ii) the aqueous composition furthercomprises a chelating agent; and/or (iii) the aqueous compositioncomprises a disaccharide at 5-20% (w/v).
 81. The method according toclaim 80, wherein: (i) the disaccharide is trehalose or thepolysaccharide is dextran, and/or (ii) the chelating agent is EDTA;and/or (iii) the chelating agent is at 80 μM to 10 mM; and/or (iv) theaqueous composition comprises trehalose, HEPES, and EDTA.
 82. The methodaccording to claim 80, wherein the aqueous composition comprises 10%trehalose (w/v), 2.8 mM HEPES, 80 μM EDTA, pH 7.1.